rs999

Homo sapiens
C>G
PBX2 : 3 Prime UTR Variant
AGER : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
None (
chr6:32186109 (GRCh38.p7) (6p21.32)
ND
GWASdb2
3   publication(s)
See rs on genome
126 Enhancers around
96 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.32186109C>G
GRCh37.p13 chr 6NC_000006.11:g.32153886C>G
AGER RefSeqGeneNG_029868.1:g.3214G>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.3624458C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.3624564C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.3502314C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.3501612C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.3409307C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.3414903C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.3491087C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.3496707C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.2:g.3518708C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.1:g.3468624C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.3528125C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.3533710C>G

Gene: PBX2, pre-B-cell leukemia homeobox 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PBX2 transcriptNM_002586.4:c.N/A3 Prime UTR Variant

Gene: AGER, advanced glycosylation end product-specific receptor(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
AGER transcript variant 1NM_001136.4:c.N/AUpstream Transcript Variant
AGER transcript variant 2NM_001206929.1:c.N/AUpstream Transcript Variant
AGER transcript variant 3NM_001206932.1:c.N/AUpstream Transcript Variant
AGER transcript variant 4NM_001206934.1:c.N/AUpstream Transcript Variant
AGER transcript variant 5NM_001206936.1:c.N/AUpstream Transcript Variant
AGER transcript variant 6NM_001206940.1:c.N/AUpstream Transcript Variant
AGER transcript variant 8NM_001206954.1:c.N/AUpstream Transcript Variant
AGER transcript variant 9NM_001206966.1:c.N/AUpstream Transcript Variant
AGER transcript variant 7NM_172197.2:c.N/AUpstream Transcript Variant
AGER transcript variant 10NR_038190.1:n.N/AUpstream Transcript Variant
AGER transcript variant X1XM_017010328.1:c.N/AUpstream Transcript Variant
AGER transcript variant X2XR_001743189.1:n.N/AUpstream Transcript Variant
AGER transcript variant X3XR_001743190.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
PMID Title Author Journal
18565990Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence.Saccone SFBioinformatics
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet
20410730Suggestive linkage of the child behavior checklist juvenile bipolar disorder phenotype to 1p21, 6p21, and 8q21.Doyle AEJ Am Acad Child Adolesc Psychiatry

P-Value

SNP ID p-value Traits Study
rs9991.42E-05nicotine dependence17158188

eQTL of rs999 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 rs999 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 )
chr63213140432132029E067-21857
chr63213204232132473E067-21413
chr63213712732137260E067-16626
chr63213741432137579E067-16307
chr63214170332141762E067-12124
chr63214176932141842E067-12044
chr63214191632141966E067-11920
chr63214233532142389E067-11497
chr63215534932155418E0671463
chr63215553232155614E0671646
chr63215593232156067E0672046
chr63215610732156162E0672221
chr63216207032162425E0678184
chr63211461732114728E068-39158
chr63213119332131243E068-22643
chr63213140432132029E068-21857
chr63213204232132473E068-21413
chr63214037332141457E068-12429
chr63214233532142389E068-11497
chr63214762532147697E068-6189
chr63214774032147794E068-6092
chr63214791032147963E068-5923
chr63215078832150865E068-3021
chr63215100832151063E068-2823
chr63215114932151415E068-2471
chr63215142332151546E068-2340
chr63215155732151682E068-2204
chr63215172232151814E068-2072
chr63215448632154586E068600
chr63215484532155067E068959
chr63215514032155200E0681254
chr63215534932155418E0681463
chr63215553232155614E0681646
chr63215593232156067E0682046
chr63215610732156162E0682221
chr63216207032162425E0688184
chr63217130832171535E06817422
chr63213119332131243E069-22643
chr63213140432132029E069-21857
chr63213204232132473E069-21413
chr63214191632141966E069-11920
chr63214233532142389E069-11497
chr63215610732156162E0692221
chr63216207032162425E0698184
chr63212363332123686E070-30200
chr63214037332141457E070-12429
chr63214233532142389E070-11497
chr63214762532147697E070-6189
chr63214774032147794E070-6092
chr63214791032147963E070-5923
chr63214871032148806E070-5080
chr63214883932148935E070-4951
chr63214903932149094E070-4792
chr63214981132149900E070-3986
chr63214998332150129E070-3757
chr63215484532155067E070959
chr63215514032155200E0701254
chr63215534932155418E0701463
chr63215925132159583E0705365
chr63215959732159659E0705711
chr63216195132162016E0708065
chr63216207032162425E0708184
chr63212363332123686E071-30200
chr63213119332131243E071-22643
chr63214762532147697E071-6189
chr63214774032147794E071-6092
chr63215484532155067E071959
chr63215514032155200E0711254
chr63215534932155418E0711463
chr63215553232155614E0711646
chr63215593232156067E0712046
chr63215610732156162E0712221
chr63216207032162425E0718184
chr63220280532202982E07148919
chr63213119332131243E072-22643
chr63213140432132029E072-21857
chr63213204232132473E072-21413
chr63214233532142389E072-11497
chr63215142332151546E072-2340
chr63213140432132029E073-21857
chr63213204232132473E073-21413
chr63214037332141457E073-12429
chr63214170332141762E073-12124
chr63214176932141842E073-12044
chr63214191632141966E073-11920
chr63214233532142389E073-11497
chr63214762532147697E073-6189
chr63214774032147794E073-6092
chr63214791032147963E073-5923
chr63215484532155067E073959
chr63215514032155200E0731254
chr63215534932155418E0731463
chr63215553232155614E0731646
chr63215593232156067E0732046
chr63215610732156162E0732221
chr63216207032162425E0738184
chr63213119332131243E074-22643
chr63213140432132029E074-21857
chr63213204232132473E074-21413
chr63214233532142389E074-11497
chr63216207032162425E0748184
chr63210478932104834E081-49052
chr63212363332123686E081-30200
chr63214762532147697E081-6189
chr63214774032147794E081-6092
chr63214791032147963E081-5923
chr63215345232153509E081-377
chr63215351132153766E081-120
chr63215925132159583E0815365
chr63215959732159659E0815711
chr63216195132162016E0818065
chr63216207032162425E0818184
chr63212363332123686E082-30200
chr63214037332141457E082-12429
chr63214791032147963E082-5923
chr63214871032148806E082-5080
chr63214883932148935E082-4951
chr63214903932149094E082-4792
chr63215448632154586E082600
chr63215484532155067E082959
chr63215514032155200E0821254
chr63215534932155418E0821463
chr63215553232155614E0821646
chr63215593232156067E0822046
chr63216195132162016E0828065
chr63216207032162425E0828184










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63211774032118318E067-35568
chr63211832632118549E067-35337
chr63211863132118770E067-35116
chr63212072732122781E067-31105
chr63214303232146367E067-7519
chr63214639832146872E067-7014
chr63215755932157851E0673673
chr63215790332159054E0674017
chr63215968032160003E0675794
chr63216265032165555E0678764
chr63211774032118318E068-35568
chr63211832632118549E068-35337
chr63211863132118770E068-35116
chr63212072732122781E068-31105
chr63214303232146367E068-7519
chr63214639832146872E068-7014
chr63215755932157851E0683673
chr63215790332159054E0684017
chr63215968032160003E0685794
chr63216265032165555E0688764
chr63211774032118318E069-35568
chr63211832632118549E069-35337
chr63211863132118770E069-35116
chr63212072732122781E069-31105
chr63214303232146367E069-7519
chr63214639832146872E069-7014
chr63215755932157851E0693673
chr63215790332159054E0694017
chr63215968032160003E0695794
chr63216265032165555E0698764
chr63211595432116004E070-37882
chr63211608332116139E070-37747
chr63211706932117119E070-36767
chr63211774032118318E070-35568
chr63211832632118549E070-35337
chr63211863132118770E070-35116
chr63212072732122781E070-31105
chr63214303232146367E070-7519
chr63214639832146872E070-7014
chr63215755932157851E0703673
chr63215790332159054E0704017
chr63216265032165555E0708764
chr63211617932116987E071-36899
chr63211774032118318E071-35568
chr63211832632118549E071-35337
chr63211863132118770E071-35116
chr63212072732122781E071-31105
chr63214303232146367E071-7519
chr63214639832146872E071-7014
chr63215755932157851E0713673
chr63215790332159054E0714017
chr63215968032160003E0715794
chr63216265032165555E0718764
chr63211706932117119E072-36767
chr63211774032118318E072-35568
chr63211832632118549E072-35337
chr63211863132118770E072-35116
chr63212072732122781E072-31105
chr63214303232146367E072-7519
chr63214639832146872E072-7014
chr63215755932157851E0723673
chr63215790332159054E0724017
chr63216265032165555E0728764
chr63211774032118318E073-35568
chr63211832632118549E073-35337
chr63211863132118770E073-35116
chr63212072732122781E073-31105
chr63214303232146367E073-7519
chr63214639832146872E073-7014
chr63215755932157851E0733673
chr63215790332159054E0734017
chr63216265032165555E0738764
chr63211863132118770E074-35116
chr63212072732122781E074-31105
chr63214303232146367E074-7519
chr63214639832146872E074-7014
chr63215755932157851E0743673
chr63215790332159054E0744017
chr63216265032165555E0748764
chr63212072732122781E081-31105
chr63214303232146367E081-7519
chr63214639832146872E081-7014
chr63216265032165555E0818764
chr63211595432116004E082-37882
chr63211608332116139E082-37747
chr63211617932116987E082-36899
chr63211706932117119E082-36767
chr63211774032118318E082-35568
chr63211832632118549E082-35337
chr63211863132118770E082-35116
chr63212072732122781E082-31105
chr63214303232146367E082-7519
chr63214639832146872E082-7014
chr63215755932157851E0823673
chr63215790332159054E0824017
chr63216265032165555E0828764