SNP Report

Basic Info
Name |
rs4460839
dbSNP
Ensembl
|
Location |
11:113451074 - 113451074(+) |
Variant Seq |
T |
Ancestral Allele |
T |
Ref Seq |
C |
Minor Allele Frequence |
0.247404 |
Annotation |
upstream_gene_variant; intron_variant; non_coding_transcript_variant
|
Variant Effect |
upstream_gene_variant(ENST00000577203, ENST00000543292); intron_variant(ENST00000540600, ENST00000346454, ENST00000542616, ENST00000362072); non_coding_transcript_variant(ENST00000540600)
|
SIFT Annotation |
tolerated
|
SIFT Variant Effect |
tolerated(ENST00000362072, ENST00000543292, ENST00000538967, ENST00000544518, ENST00000542968, ENST00000346454)
|
PolyPhen Annotation |
benign
|
PolyPhen Variant Effect |
benign(ENST00000362072, ENST00000543292, ENST00000538967, ENST00000544518, ENST00000542968, ENST00000346454)
|
rSNP? |
Yes
Link in rVarBase
|
Related Regulatory Elements |
n/a
|
Chromatin State |
Weak transcription
|
No. of Marker's Association Results |
1 (Positive: 0; Negative: 1; Trend: 0) |
Source |
Literature |

SNP related association results

SNP related genes (count: 2)

SNPs in LD with rs4460839 (count: 12)
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] |
rs4274224
|
downstream_gene_variant(ENST00000577203); upstream_gene_variant(ENST00000543292); intron_variant(ENST00000346454, ENST00000362072, ENST00000542616, ENST00000540600); non_coding_transcript_variant(ENST00000540600) |
1(0/1/0)
|
0.8548[ASN] |
LD-proxies (count: 11)

rs_ID |
Literature-origin SNPs with LD |
Annotation |
r2[population] |
rs4936272
|
rs4274224
rs4460839
|
downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.8548[ASN] |
rs10891553
|
rs4460839
|
intron_variant; non_coding_transcript_variant |
0.8096[ASN] |
rs4245147
|
rs4274224
rs4460839
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.8548[ASN] |
rs11214612
|
rs4460839
|
intron_variant; non_coding_transcript_variant |
0.8096[ASN] |
rs4581480
|
rs4460839
|
upstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9675[ASN] |
rs4936274
|
rs4460839
|
intron_variant; non_coding_transcript_variant |
0.8096[ASN] |
rs4936270
|
rs4460839
|
downstream_gene_variant; 5_prime_UTR_variant; intron_variant; non_coding_transcript_variant |
1.0000[ASN] |
rs4245148
|
rs4460839
|
downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant |
1.0000[ASN] |
rs4936271
|
rs4274224
rs4460839
|
downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.8548[ASN] |
rs11214613
|
rs4460839
|
intron_variant; non_coding_transcript_variant |
0.8096[ASN] |
rs4245146
|
rs4274224
rs4460839
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.8548[ASN] |

SNP related eQTL (count: 1)