SNP Report

Basic Info
Name |
rs4792887
dbSNP
Ensembl
|
Location |
17:45799654 - 45799654(+) |
Variant Seq |
T |
Ancestral Allele |
C |
Ref Seq |
C |
Minor Allele Frequence |
0.129992 |
Annotation |
non_coding_transcript_exon_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
|
Variant Effect |
non_coding_transcript_exon_variant(ENST00000634876); intron_variant(ENST00000634540, ENST00000577353, ENST00000398285, ENST00000293493, ENST00000347197, ENST00000587305, ENST00000339069, ENST00000582766, ENST00000352855, ENST00000314537, ENST00000619154); NMD_transcript_variant(ENST00000347197); non_coding_transcript_variant(ENST00000587305, ENST00000634876, ENST00000582766)
|
SIFT Annotation |
deleterious; tolerated
|
SIFT Variant Effect |
deleterious(ENST00000430334); tolerated(ENST00000430334, ENST00000581448, ENST00000584420, ENST00000589780)
|
PolyPhen Annotation |
benign; possibly_damaging
|
PolyPhen Variant Effect |
benign(ENST00000430334, ENST00000581448, ENST00000584420, ENST00000589780); possibly_damaging(ENST00000430334, ENST00000584420)
|
rSNP? |
Yes
Link in rVarBase
|
Related Regulatory Elements |
n/a
|
Chromatin State |
Weak transcription
|
No. of Marker's Association Results |
2 (Positive: 1; Negative: 1; Trend: 0) |
Source |
Literature |

SNP related association results

SNP related genes (count: 2)

SNPs in LD with rs4792887 (count: 14)
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: 1)

|
rs_ID |
Annotation |
No. of Association Results(Positive/Negative/Trend) |
r2[population] |
rs12936181
|
downstream_gene_variant(ENST00000634876); intron_variant(ENST00000352855, ENST00000339069, ENST00000634540, ENST00000619154, ENST00000347197, ENST00000293493, ENST00000577353, ENST00000587305, ENST00000314537, ENST00000398285, ENST00000582766); NMD_transcript_variant(ENST00000347197); non_coding_transcript_variant(ENST00000587305, ENST00000582766) |
1(0/1/0)
|
1.0000[EUR]; 1.0000[AFR]; 1.0000[AMR] |
LD-proxies (count: 13)

rs_ID |
Literature-origin SNPs with LD |
Annotation |
r2[population] |
rs4792888
|
rs12936181
rs4792887
|
non_coding_transcript_exon_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
1.0000[EUR]; 0.9578[AFR]; 1.0000[AMR] |
rs16940646
|
rs12936181
rs4792887
|
upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
1.0000[EUR]; 0.8196[AFR]; 0.9648[AMR] |
rs35131568
|
rs12936181
rs4792887
|
downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
0.9461[EUR]; 0.9914[AFR]; 1.0000[AMR] |
rs4792883
|
rs12936181
rs4792887
|
downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
1.0000[EUR]; 1.0000[AFR]; 1.0000[AMR] |
rs12945673
|
rs12936181
rs4792887
|
intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
1.0000[EUR]; 0.9829[AFR]; 1.0000[AMR] |
rs35785975
|
rs12936181
rs4792887
|
downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
1.0000[EUR]; 0.8938[AFR]; 0.9658[AMR] |
rs16969853
|
rs12936181
rs4792887
|
upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
1.0000[EUR]; 0.9492[AFR]; 1.0000[AMR] |
rs4792884
|
rs12936181
rs4792887
|
downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
1.0000[EUR]; 0.9497[AFR]; 1.0000[AMR] |
rs4792885
|
rs12936181
rs4792887
|
downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
0.8705[EUR]; 0.9572[AFR]; 0.9035[AMR] |
rs12942994
|
rs12936181
rs4792887
|
downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
0.9461[EUR]; 0.9914[AFR]; 1.0000[AMR] |
rs4792886
|
rs12936181
rs4792887
|
non_coding_transcript_exon_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
1.0000[EUR]; 0.9243[AFR]; 0.9648[AMR] |
rs12944996
|
rs12936181
rs4792887
|
downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
1.0000[EUR]; 1.0000[AFR]; 1.0000[AMR] |
rs34174655
|
rs12936181
rs4792887
|
downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
0.8546[EUR] |

SNP related eQTL (count: 1)