SNP Report

Basic Info
Name |
rs10002308
dbSNP
Ensembl
|
Location |
4:168478672 - 168478672(+) |
Variant Seq |
A |
Ancestral Allele |
A |
Ref Seq |
C |
Minor Allele Frequence |
0.389976 |
Annotation |
intron_variant; non_coding_transcript_variant
|
Variant Effect |
intron_variant(ENST00000511577, ENST00000515088, ENST00000260184, ENST00000514748, ENST00000512371, ENST00000505696, ENST00000513901, ENST00000505890, ENST00000505150); non_coding_transcript_variant(ENST00000515088, ENST00000513901, ENST00000505150)
|
SIFT Annotation |
deleterious
|
SIFT Variant Effect |
deleterious(ENST00000512371, ENST00000505696, ENST00000514748, ENST00000511577, ENST00000505890, ENST00000260184)
|
PolyPhen Annotation |
probably_damaging
|
PolyPhen Variant Effect |
probably_damaging(ENST00000512371, ENST00000505696, ENST00000514748, ENST00000511577, ENST00000505890, ENST00000260184)
|
rSNP? |
Yes
Link in rVarBase
|
Related Regulatory Elements |
n/a
|
Chromatin State |
Weak transcription;Active TSS;Enhancers;Flanking Active TSS;Genic enhancers
|
No. of Marker's Association Results |
1 (Positive: 0; Negative: 0; Trend: 1) |
Source |
Literature |

SNP related association results

SNP related genes (count: 1)

SNPs in LD with rs10002308 (count: 9)
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: 9)

rs_ID |
Literature-origin SNPs with LD |
Annotation |
r2[population] |
rs2710832
|
rs10002308
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9658[EUR]; 0.8527[AFR]; 0.9472[AMR] |
rs28524000
|
rs10002308
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9489[EUR]; 0.9346[AMR] |
rs12331721
|
rs10002308
|
intron_variant; non_coding_transcript_variant |
0.8374[EUR]; 0.8461[AMR] |
rs55764504
|
rs10002308
|
intron_variant; non_coding_transcript_variant |
0.8215[EUR]; 0.8339[AMR] |
rs28675009
|
rs10002308
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9489[EUR]; 0.8690[AFR]; 0.9735[AMR] |
rs2710831
|
rs10002308
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9658[EUR]; 0.8770[AFR]; 0.9472[AMR] |
rs13353710
|
rs10002308
|
intron_variant; non_coding_transcript_variant |
0.9771[EUR]; 0.9838[AFR]; 1.0000[AMR] |
rs17054232
|
rs10002308
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.8098[AMR] |
rs9999142
|
rs10002308
|
intron_variant; non_coding_transcript_variant |
0.8272[EUR] |

SNP related eQTL (count: 1)