Variant report

Variant	rs7032393
Chromosome Location	chr9:18458688-18458689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1006022	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10453192	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10733354	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10738511	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10756963	0.95[ASN][1000 genomes]
rs10756964	0.99[ASN][1000 genomes]
rs10810969	0.87[ASN][1000 genomes]
rs10810971	0.99[ASN][1000 genomes]
rs10810973	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10963613	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11793923	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1281350	0.83[CHB][hapmap]
rs1281352	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1329721	0.92[ASN][1000 genomes]
rs1340039	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1340040	0.90[ASN][1000 genomes]
rs1340042	0.98[ASN][1000 genomes]
rs1340043	0.95[ASN][1000 genomes]
rs1417035	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1417037	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1538999	0.89[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs1576383	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16936745	0.89[CEU][hapmap]
rs1832747	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1888068	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1888069	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2149875	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs2153414	0.94[ASN][1000 genomes]
rs2153415	0.96[CEU][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2153416	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2277160	0.82[EUR][1000 genomes]
rs3898100	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4246142	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4246143	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4590536	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4961651	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4961652	0.96[CEU][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6475216	0.92[ASN][1000 genomes]
rs6475218	0.87[ASN][1000 genomes]
rs6475219	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6475220	0.96[CEU][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6475221	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7019399	0.96[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7036515	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7046502	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856703	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7867766	0.96[CEU][hapmap];0.82[CHD][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831522	chr9:18231982-18459492	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv892688	chr9:18385143-18551247	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7032393	CNTLN	cis	cerebellum	SCAN
rs7032393	FREM1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18456800-18458800	Enhancers	NHDF-Ad	bronchial
2	chr9:18456800-18459600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:18456800-18459800	Enhancers	HUVEC	blood vessel
4	chr9:18457000-18459800	Enhancers	NHEK	skin
5	chr9:18457200-18459000	Weak transcription	Fetal Intestine Large	intestine
6	chr9:18457200-18461600	Enhancers	HMEC	breast
7	chr9:18457600-18460400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:18457800-18459400	Weak transcription	NH-A	brain
9	chr9:18457800-18463800	Weak transcription	NHLF	lung
10	chr9:18458000-18459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:18458000-18459200	Weak transcription	Osteobl	bone
12	chr9:18458000-18459400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:18458000-18459600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:18458000-18463800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:18458200-18459200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr9:18458200-18459200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:18458200-18459400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:18458200-18460200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:18458600-18458800	Enhancers	Fetal Intestine Small	intestine
20	chr9:18458600-18458800	Enhancers	Hela-S3	cervix
21	chr9:18458600-18459800	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links