SNP Report

Basic Info
Name |
rs173365
dbSNP
Ensembl
|
Location |
17:45823708 - 45823708(+) |
Variant Seq |
G |
Ancestral Allele |
A |
Ref Seq |
A |
Minor Allele Frequence |
0.348043 |
Annotation |
intron_variant; NMD_transcript_variant; non_coding_transcript_variant
|
Variant Effect |
intron_variant(ENST00000293493, ENST00000583888, ENST00000352855, ENST00000398285, ENST00000619154, ENST00000339069, ENST00000314537, ENST00000580955, ENST00000347197, ENST00000577353, ENST00000634540, ENST00000634876, ENST00000582766); NMD_transcript_variant(ENST00000583888, ENST00000580955, ENST00000347197); non_coding_transcript_variant(ENST00000634876, ENST00000582766)
|
SIFT Annotation |
deleterious_-_low_confidence; deleterious; tolerated
|
SIFT Variant Effect |
deleterious_-_low_confidence(ENST00000619154); deleterious(ENST00000339069, ENST00000293493, ENST00000398285, ENST00000634540); tolerated(ENST00000314537, ENST00000352855, ENST00000577353)
|
PolyPhen Annotation |
unknown; benign; possibly_damaging
|
PolyPhen Variant Effect |
unknown(ENST00000619154); benign(ENST00000339069, ENST00000293493, ENST00000352855, ENST00000398285, ENST00000634540, ENST00000577353); possibly_damaging(ENST00000314537)
|
rSNP? |
Yes
Link in rVarBase
|
Related Regulatory Elements |
n/a
|
Chromatin State |
Enhancers;Bivalent Enhancer;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: 2)

SNPs in LD with rs173365 (count: 6)
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] |
rs17689966
|
downstream_gene_variant(ENST00000580955, ENST00000582766); upstream_gene_variant(ENST00000535778, ENST00000580876); intron_variant(ENST00000583888, ENST00000619154, ENST00000398285, ENST00000634540, ENST00000634876, ENST00000581479, ENST00000293493, ENST00000352855, ENST00000339069, ENST00000314537, ENST00000347197, ENST00000577353); NMD_transcript_variant(ENST00000583888, ENST00000347197); non_coding_transcript_variant(ENST00000634876, ENST00000581479) |
1(1/0/0)
|
0.9946[EUR]; 0.9441[AMR] |
LD-proxies (count: 5)

rs_ID |
Literature-origin SNPs with LD |
Annotation |
r2[population] |
rs242948
|
rs173365
rs17689966
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9839[EUR]; 0.9009[AMR] |
rs242937
|
rs173365
rs17689966
|
downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
1.0000[EUR]; 1.0000[AFR]; 1.0000[AMR] |
rs242947
|
rs173365
rs17689966
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9892[EUR]; 0.8905[AMR] |
rs242944
|
rs173365
rs17689966
|
missense_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9892[EUR]; 0.8905[AMR] |
rs242951
|
rs173365
rs17689966
|
downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant |
0.9840[EUR]; 0.9774[AMR] |

SNP related eQTL (count: 1)