rs2961663

Homo sapiens
C>G / C>T
GMCL1P1 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0140 (4195/29964,GnomAD)
T=0154 (4500/29118,TOPMED)
T=0109 (545/5008,1000G)
T=0110 (423/3854,ALSPAC)
T=0100 (371/3708,TWINSUK)
chr5:178186543 (GRCh38.p7) (5q35.3)
AD
GWASdb2
2   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.178186543C>G
GRCh38.p7 chr 5NC_000005.10:g.178186543C>T
GRCh37.p13 chr 5NC_000005.9:g.177613544C>G
GRCh37.p13 chr 5NC_000005.9:g.177613544C>T

Gene: GMCL1P1, germ cell-less, spermatogenesis associated 1 pseudogene 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
Non-protein-coding transcriptsNR_003281.1:n.890G>CG>CNon Coding Transcript Variant
Non-protein-coding transcriptsNR_003281.1:n.890G>AG>ANon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.759T=0.241
1000GenomesAmericanSub694C=0.910T=0.090
1000GenomesEast AsianSub1008C=0.978T=0.022
1000GenomesEuropeSub1006C=0.920T=0.080
1000GenomesGlobalStudy-wide5008C=0.891T=0.109
1000GenomesSouth AsianSub978C=0.940T=0.060
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.890T=0.110
The Genome Aggregation DatabaseAfricanSub8718C=0.757T=0.243
The Genome Aggregation DatabaseAmericanSub834C=0.920T=0.080
The Genome Aggregation DatabaseEast AsianSub1620C=0.998T=0.002
The Genome Aggregation DatabaseEuropeSub18490C=0.892T=0.107
The Genome Aggregation DatabaseGlobalStudy-wide29964C=0.860T=0.140
The Genome Aggregation DatabaseOtherSub302C=0.930T=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.845T=0.154
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.900T=0.100
PMID Title Author Journal
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res
21156761A genome-wide association study suggests contrasting associations in ACPA-positive versus ACPA-negative rheumatoid arthritis.Padyukov LAnn Rheum Dis

P-Value

SNP ID p-value Traits Study
rs29616639.83E-05alcohol dependence21703634

eQTL of rs2961663 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 rs2961663 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.