Variant report

Variant	rs16971223
Chromosome Location	chr15:41214281-41214282
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12439845	0.90[JPT][hapmap]
rs12591675	0.81[EUR][1000 genomes]
rs16971222	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs28434362	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212278	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4923888	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60237220	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492971	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7164358	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv904104	chr15:41149824-41234932	Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	esv1819792	chr15:41184722-41234825	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16971223	GPR176	cis	parietal	SCAN
rs16971223	RASGRP1	cis	parietal	SCAN
rs16971223	BMF	cis	parietal	SCAN
rs16971223	GCHFR	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41203600-41214400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:41206600-41214400	Weak transcription	Fetal Kidney	kidney
3	chr15:41209600-41215800	Enhancers	Fetal Intestine Large	intestine
4	chr15:41209800-41216000	Enhancers	Fetal Intestine Small	intestine
5	chr15:41210600-41214600	Weak transcription	Colonic Mucosa	Colon
6	chr15:41211600-41218000	Weak transcription	Right Atrium	heart
7	chr15:41211800-41214800	Weak transcription	Lung	lung
8	chr15:41211800-41218200	Weak transcription	Brain Anterior Caudate	brain
9	chr15:41212000-41214400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr15:41212000-41214400	Weak transcription	HUVEC	blood vessel
11	chr15:41212200-41214800	Weak transcription	Right Ventricle	heart
12	chr15:41212400-41214400	Enhancers	HepG2	liver
13	chr15:41214000-41215600	Enhancers	Duodenum Mucosa	Duodenum
14	chr15:41214200-41214400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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