rs12980993

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

LILRA1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0227 (6810/29908,GnomAD)
C=0277 (8077/29118,TOPMED)
C=0294 (1470/5008,1000G)
C=0106 (410/3854,ALSPAC)
C=0103 (382/3708,TWINSUK)

Position: chr19:54593944 (GRCh38.p7) (19q13.42)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 261 Enhancers around

Promoter: 51 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.54593944A>C
GRCh37.p13 chr 19 fix patch HG1079_PATCH	NW_004166865.1:g.568311A>C
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1	NT_187693.1:g.576523A>C
GRCh37.p13 chr 19	NC_000019.9:g.55105409A>C
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1	NW_003571060.1:g.498828A>C
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1	NW_003571054.1:g.500334A>C

Gene: LILRA1, leukocyte immunoglobulin like receptor A1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LILRA1 transcript variant 2	NM_001278318.1:c.	N/A	Intron Variant
LILRA1 transcript variant 1	NM_006863.3:c.	N/A	Intron Variant
LILRA1 transcript variant 3	NM_001278319.1:c.	N/A	Genic Upstream Transcript Variant
LILRA1 transcript variant 4	NR_103501.1:n.	N/A	Intron Variant
LILRA1 transcript variant 5	NR_103502.1:n.	N/A	Intron Variant
LILRA1 transcript variant 6	NR_103503.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.481	C=0.519
1000Genomes	American	Sub	694	A=0.730	C=0.270
1000Genomes	East Asian	Sub	1008	A=0.722	C=0.278
1000Genomes	Europe	Sub	1006	A=0.897	C=0.103
1000Genomes	Global	Study-wide	5008	A=0.706	C=0.294
1000Genomes	South Asian	Sub	978	A=0.780	C=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.894	C=0.106
The Genome Aggregation Database	African	Sub	8688	A=0.534	C=0.466
The Genome Aggregation Database	American	Sub	838	A=0.750	C=0.250
The Genome Aggregation Database	East Asian	Sub	1618	A=0.694	C=0.306
The Genome Aggregation Database	Europe	Sub	18462	A=0.890	C=0.109
The Genome Aggregation Database	Global	Study-wide	29908	A=0.772	C=0.227
The Genome Aggregation Database	Other	Sub	302	A=0.870	C=0.130
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.722	C=0.277
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.897	C=0.103

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs12980993	0.000705	alcohol dependence	21314694

eQTL of rs12980993 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs12980993 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr19	534509	534565	E067	-33746
chr19	534777	534827	E067	-33484
chr19	534901	535052	E067	-33259
chr19	535090	535426	E067	-32885
chr19	535533	535846	E067	-32465
chr19	551174	551336	E067	-16975
chr19	551366	551552	E067	-16759
chr19	574107	574278	E067	5796
chr19	576737	576824	E067	8426
chr19	576862	577212	E067	8551
chr19	577228	577350	E067	8917
chr19	577399	577504	E067	9088
chr19	577519	577623	E067	9208
chr19	577665	577879	E067	9354
chr19	577905	577955	E067	9594
chr19	578009	578184	E067	9698
chr19	579826	579966	E067	11515
chr19	580036	580097	E067	11725
chr19	580161	580257	E067	11850
chr19	607648	607712	E067	39337
chr19	607822	608011	E067	39511
chr19	608126	608176	E067	39815
chr19	608191	608287	E067	39880
chr19	608362	608412	E067	40051
chr19	608455	608620	E067	40144
chr19	608860	609073	E067	40549
chr19	609080	609269	E067	40769
chr19	609288	609385	E067	40977
chr19	609466	609516	E067	41155
chr19	609545	609595	E067	41234
chr19	609775	609856	E067	41464
chr19	609988	610125	E067	41677
chr19	534509	534565	E068	-33746
chr19	551174	551336	E068	-16975
chr19	551366	551552	E068	-16759
chr19	576737	576824	E068	8426
chr19	576862	577212	E068	8551
chr19	577228	577350	E068	8917
chr19	577399	577504	E068	9088
chr19	583747	585118	E068	15436
chr19	607255	607309	E068	38944
chr19	607360	607420	E068	39049
chr19	607648	607712	E068	39337
chr19	607822	608011	E068	39511
chr19	608126	608176	E068	39815
chr19	608191	608287	E068	39880
chr19	608362	608412	E068	40051
chr19	608455	608620	E068	40144
chr19	608860	609073	E068	40549
chr19	609080	609269	E068	40769
chr19	609288	609385	E068	40977
chr19	609466	609516	E068	41155
chr19	609545	609595	E068	41234
chr19	534509	534565	E069	-33746
chr19	534777	534827	E069	-33484
chr19	534901	535052	E069	-33259
chr19	535090	535426	E069	-32885
chr19	535533	535846	E069	-32465
chr19	537974	538060	E069	-30251
chr19	538186	538356	E069	-29955
chr19	538422	538476	E069	-29835
chr19	558802	559122	E069	-9189
chr19	559207	559257	E069	-9054
chr19	559311	559411	E069	-8900
chr19	576737	576824	E069	8426
chr19	577399	577504	E069	9088
chr19	577519	577623	E069	9208
chr19	579478	579638	E069	11167
chr19	579705	579785	E069	11394
chr19	579826	579966	E069	11515
chr19	580036	580097	E069	11725
chr19	580161	580257	E069	11850
chr19	580365	580598	E069	12054
chr19	583747	585118	E069	15436
chr19	607255	607309	E069	38944
chr19	607360	607420	E069	39049
chr19	607648	607712	E069	39337
chr19	607822	608011	E069	39511
chr19	608126	608176	E069	39815
chr19	608191	608287	E069	39880
chr19	608362	608412	E069	40051
chr19	608455	608620	E069	40144
chr19	608860	609073	E069	40549
chr19	609080	609269	E069	40769
chr19	609288	609385	E069	40977
chr19	609466	609516	E069	41155
chr19	609545	609595	E069	41234
chr19	609775	609856	E069	41464
chr19	609988	610125	E069	41677
chr19	534901	535052	E070	-33259
chr19	535090	535426	E070	-32885
chr19	535533	535846	E070	-32465
chr19	535898	535948	E070	-32363
chr19	576737	576824	E070	8426
chr19	534509	534565	E071	-33746
chr19	534777	534827	E071	-33484
chr19	534901	535052	E071	-33259
chr19	535090	535426	E071	-32885
chr19	535533	535846	E071	-32465
chr19	574107	574278	E071	5796
chr19	576737	576824	E071	8426
chr19	576862	577212	E071	8551
chr19	577228	577350	E071	8917
chr19	577399	577504	E071	9088
chr19	577519	577623	E071	9208
chr19	577665	577879	E071	9354
chr19	577905	577955	E071	9594
chr19	578009	578184	E071	9698
chr19	578233	578277	E071	9922
chr19	578341	578393	E071	10030
chr19	579208	579268	E071	10897
chr19	579478	579638	E071	11167
chr19	579705	579785	E071	11394
chr19	579826	579966	E071	11515
chr19	580036	580097	E071	11725
chr19	580161	580257	E071	11850
chr19	580365	580598	E071	12054
chr19	583747	585118	E071	15436
chr19	594222	594322	E071	25911
chr19	594375	594415	E071	26064
chr19	607255	607309	E071	38944
chr19	607360	607420	E071	39049
chr19	607648	607712	E071	39337
chr19	607822	608011	E071	39511
chr19	608126	608176	E071	39815
chr19	608191	608287	E071	39880
chr19	608362	608412	E071	40051
chr19	608455	608620	E071	40144
chr19	608860	609073	E071	40549
chr19	609080	609269	E071	40769
chr19	609288	609385	E071	40977
chr19	609466	609516	E071	41155
chr19	609545	609595	E071	41234
chr19	609775	609856	E071	41464
chr19	609988	610125	E071	41677
chr19	610473	611892	E071	42162
chr19	534509	534565	E072	-33746
chr19	534777	534827	E072	-33484
chr19	534901	535052	E072	-33259
chr19	535090	535426	E072	-32885
chr19	537974	538060	E072	-30251
chr19	538186	538356	E072	-29955
chr19	551366	551552	E072	-16759
chr19	574107	574278	E072	5796
chr19	577228	577350	E072	8917
chr19	577399	577504	E072	9088
chr19	577519	577623	E072	9208
chr19	577665	577879	E072	9354
chr19	577905	577955	E072	9594
chr19	578009	578184	E072	9698
chr19	578233	578277	E072	9922
chr19	578341	578393	E072	10030
chr19	578520	578601	E072	10209
chr19	578612	578687	E072	10301
chr19	578938	578988	E072	10627
chr19	579208	579268	E072	10897
chr19	579478	579638	E072	11167
chr19	579705	579785	E072	11394
chr19	579826	579966	E072	11515
chr19	580036	580097	E072	11725
chr19	580161	580257	E072	11850
chr19	580365	580598	E072	12054
chr19	607255	607309	E072	38944
chr19	607360	607420	E072	39049
chr19	607648	607712	E072	39337
chr19	607822	608011	E072	39511
chr19	608126	608176	E072	39815
chr19	608191	608287	E072	39880
chr19	608362	608412	E072	40051
chr19	608455	608620	E072	40144
chr19	608860	609073	E072	40549
chr19	609080	609269	E072	40769
chr19	609288	609385	E072	40977
chr19	609466	609516	E072	41155
chr19	609545	609595	E072	41234
chr19	609775	609856	E072	41464
chr19	609988	610125	E072	41677
chr19	610473	611892	E072	42162
chr19	534509	534565	E073	-33746
chr19	534777	534827	E073	-33484
chr19	534901	535052	E073	-33259
chr19	535090	535426	E073	-32885
chr19	535533	535846	E073	-32465
chr19	538958	539008	E073	-29303
chr19	539021	539078	E073	-29233
chr19	539157	539275	E073	-29036
chr19	539377	539483	E073	-28828
chr19	556697	556915	E073	-11396
chr19	556944	556988	E073	-11323
chr19	559207	559257	E073	-9054
chr19	559311	559411	E073	-8900
chr19	578009	578184	E073	9698
chr19	578233	578277	E073	9922
chr19	578341	578393	E073	10030
chr19	578520	578601	E073	10209
chr19	578612	578687	E073	10301
chr19	578938	578988	E073	10627
chr19	579208	579268	E073	10897
chr19	579478	579638	E073	11167
chr19	579705	579785	E073	11394
chr19	579826	579966	E073	11515
chr19	580036	580097	E073	11725
chr19	580161	580257	E073	11850
chr19	580365	580598	E073	12054
chr19	580624	580806	E073	12313
chr19	581834	581994	E073	13523
chr19	582070	582185	E073	13759
chr19	583747	585118	E073	15436
chr19	592515	592583	E073	24204
chr19	608126	608176	E073	39815
chr19	608191	608287	E073	39880
chr19	608362	608412	E073	40051
chr19	608455	608620	E073	40144
chr19	608860	609073	E073	40549
chr19	609080	609269	E073	40769
chr19	609288	609385	E073	40977
chr19	609466	609516	E073	41155
chr19	609545	609595	E073	41234
chr19	609775	609856	E073	41464
chr19	609988	610125	E073	41677
chr19	534901	535052	E074	-33259
chr19	535090	535426	E074	-32885
chr19	574107	574278	E074	5796
chr19	575910	576488	E074	7599
chr19	576737	576824	E074	8426
chr19	576862	577212	E074	8551
chr19	579826	579966	E074	11515
chr19	580036	580097	E074	11725
chr19	580161	580257	E074	11850
chr19	583747	585118	E074	15436
chr19	602723	602863	E074	34412
chr19	607255	607309	E074	38944
chr19	607360	607420	E074	39049
chr19	607648	607712	E074	39337
chr19	607822	608011	E074	39511
chr19	608126	608176	E074	39815
chr19	608191	608287	E074	39880
chr19	608362	608412	E074	40051
chr19	608455	608620	E074	40144
chr19	608860	609073	E074	40549
chr19	609080	609269	E074	40769
chr19	609288	609385	E074	40977
chr19	609466	609516	E074	41155
chr19	609545	609595	E074	41234
chr19	609775	609856	E074	41464
chr19	609988	610125	E074	41677
chr19	610473	611892	E074	42162
chr19	534509	534565	E081	-33746
chr19	534777	534827	E081	-33484
chr19	534901	535052	E081	-33259
chr19	535090	535426	E081	-32885
chr19	551174	551336	E081	-16975
chr19	551366	551552	E081	-16759
chr19	574107	574278	E081	5796
chr19	575910	576488	E081	7599
chr19	576737	576824	E081	8426
chr19	576862	577212	E081	8551
chr19	534901	535052	E082	-33259
chr19	535090	535426	E082	-32885
chr19	535533	535846	E082	-32465
chr19	535898	535948	E082	-32363

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	530689	534451	E067	-33860
chr19	570959	573974	E067	2648
chr19	590323	590644	E067	22012
chr19	590826	590866	E067	22515
chr19	530689	534451	E068	-33860
chr19	570799	570868	E068	2488
chr19	570959	573974	E068	2648
chr19	589408	589608	E068	21097
chr19	590323	590644	E068	22012
chr19	590826	590866	E068	22515
chr19	530689	534451	E069	-33860
chr19	570959	573974	E069	2648
chr19	589408	589608	E069	21097
chr19	589777	589923	E069	21466
chr19	590050	590278	E069	21739
chr19	590323	590644	E069	22012
chr19	590826	590866	E069	22515
chr19	530689	534451	E070	-33860
chr19	570959	573974	E070	2648
chr19	589777	589923	E070	21466
chr19	590323	590644	E070	22012
chr19	530689	534451	E071	-33860
chr19	570959	573974	E071	2648
chr19	589777	589923	E071	21466
chr19	590050	590278	E071	21739
chr19	590323	590644	E071	22012
chr19	590826	590866	E071	22515
chr19	530689	534451	E072	-33860
chr19	570959	573974	E072	2648
chr19	589408	589608	E072	21097
chr19	589777	589923	E072	21466
chr19	590050	590278	E072	21739
chr19	590323	590644	E072	22012
chr19	590826	590866	E072	22515
chr19	530689	534451	E073	-33860
chr19	570959	573974	E073	2648
chr19	589408	589608	E073	21097
chr19	590323	590644	E073	22012
chr19	590826	590866	E073	22515
chr19	530689	534451	E074	-33860
chr19	570959	573974	E074	2648
chr19	589408	589608	E074	21097
chr19	590323	590644	E074	22012
chr19	590826	590866	E074	22515
chr19	570959	573974	E081	2648
chr19	530689	534451	E082	-33860
chr19	570959	573974	E082	2648
chr19	589408	589608	E082	21097
chr19	589777	589923	E082	21466
chr19	590050	590278	E082	21739
chr19	590323	590644	E082	22012