SNP Report

Basic Info
Name |
rs588765
dbSNP
Ensembl
|
Location |
15:78573083 - 78573083(+) |
Variant Seq |
C |
Ancestral Allele |
C |
Ref Seq |
T |
Minor Allele Frequence |
0.275559 |
Annotation |
intron_variant
|
Variant Effect |
intron_variant(ENST00000299565, ENST00000559554)
|
SIFT Annotation |
tolerated
|
SIFT Variant Effect |
tolerated(ENST00000044462, ENST00000413382, ENST00000559154, ENST00000559948, ENST00000559365, ENST00000560217, ENST00000559082, ENST00000560737, ENST00000558094, ENST00000558281, ENST00000559437, ENST00000559146)
|
PolyPhen Annotation |
benign
|
PolyPhen Variant Effect |
benign(ENST00000044462, ENST00000413382, ENST00000559154, ENST00000559948, ENST00000559365, ENST00000560217, ENST00000559082, ENST00000560737, ENST00000558094, ENST00000558281, ENST00000559437, ENST00000559146)
|
rSNP? |
Yes
Link in rVarBase
|
Related Regulatory Elements |
Chromatin interactive region
|
Chromatin State |
ZNF genes & repeats;Weak transcription
|
No. of Marker's Association Results |
1 (Positive: 1; Negative: 0; Trend: 0) |
Source |
Literature |

SNP related association results

SNP related genes (count: 1)

SNPs in LD with rs588765 (count: 21)
The LD data used here is based on 1000 Genome Phase I. LD SNP pairs were selected with a threshold r2<=0.8.
Literature-origin SNPs (count: 0)
LD-proxies (count: 21)

rs_ID |
Literature-origin SNPs with LD |
Annotation |
r2[population] |
rs6495307
|
rs588765
|
downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant |
0.9301[EUR]; 0.9108[AMR] |
rs601079
|
rs588765
|
upstream_gene_variant; intron_variant |
0.9728[EUR]; 0.9006[AMR] |
rs621849
|
rs588765
|
upstream_gene_variant; intron_variant |
0.9728[EUR]; 0.9006[AMR] |
rs57945453
|
rs588765
|
intron_variant |
0.8032[EUR]; 0.8232[AMR] |
rs12911602
|
rs588765
|
downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant |
0.9353[EUR]; 0.9108[AMR] |
rs12901300
|
rs588765
|
downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant |
0.9353[EUR]; 0.9108[AMR] |
rs1878399
|
rs588765
|
downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
0.9043[EUR]; 0.8297[AMR] |
rs11637635
|
rs588765
|
downstream_gene_variant; intron_variant |
0.8454[AFR]; 0.8222[AMR] |
rs481134
|
rs588765
|
downstream_gene_variant; intron_variant |
0.9566[EUR]; 0.9787[AFR]; 0.9695[AMR] |
rs647041
|
rs588765
|
downstream_gene_variant; upstream_gene_variant; intron_variant |
0.9459[EUR]; 0.9160[AFR]; 0.9546[AMR] |
rs6495306
|
rs588765
|
intron_variant |
1.0000[EUR]; 0.9894[AFR]; 1.0000[AMR] |
rs514743
|
rs588765
|
downstream_gene_variant; upstream_gene_variant; intron_variant |
0.8074[AMR] |
rs3743077
|
rs588765
|
upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
0.9353[EUR]; 0.8949[AMR] |
rs680244
|
rs588765
|
upstream_gene_variant; intron_variant |
0.9674[EUR]; 0.9006[AMR] |
rs555018
|
rs588765
|
downstream_gene_variant; upstream_gene_variant; intron_variant |
0.9566[EUR]; 0.9789[AFR]; 0.9695[AMR] |
rs660652
|
rs588765
|
downstream_gene_variant; upstream_gene_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
0.8343[AFR]; 0.8074[AMR] |
rs61012457
|
rs588765
|
intron_variant |
0.8032[EUR]; 0.8232[AMR] |
rs2456019
|
rs588765
|
upstream_gene_variant; intron_variant |
0.8074[AMR] |
rs692780
|
rs588765
|
downstream_gene_variant; intron_variant |
0.8222[AMR] |
rs8025188
|
rs588765
|
downstream_gene_variant; non_coding_transcript_exon_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
0.8732[EUR] |
rs472054
|
rs588765
|
downstream_gene_variant; upstream_gene_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
0.8343[AFR]; 0.8074[AMR] |

SNP related eQTL (count: 1)