Variant report

Variant	rs6475219
Chromosome Location	chr9:18455870-18455871
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1006022	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10453192	0.98[EUR][1000 genomes]
rs10733354	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10738510	0.96[ASN][1000 genomes]
rs10738511	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10756964	0.84[AFR][1000 genomes]
rs10810970	0.88[ASN][1000 genomes]
rs10810973	0.85[EUR][1000 genomes]
rs10963613	0.85[CEU][hapmap]
rs11793923	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1281350	0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1281352	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1340039	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1417035	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1417037	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1538999	0.89[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs16936745	0.89[CEU][hapmap]
rs1832747	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs1888068	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1888069	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2149875	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs2153415	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs2153416	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2277160	0.81[EUR][1000 genomes]
rs3898100	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4246142	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4246143	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4590536	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4961651	0.87[EUR][1000 genomes]
rs4961652	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6475220	0.96[CEU][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs6475221	0.88[EUR][1000 genomes]
rs7019399	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7032393	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7036515	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7046502	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7856703	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs7867766	0.96[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.96[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
rs6475219	CNTLN	cis	cerebellum	SCAN
rs6475219	FREM1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18443200-18457400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:18447600-18456000	Weak transcription	NHEK	skin
3	chr9:18448400-18456800	Weak transcription	NHLF	lung
4	chr9:18453000-18456600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:18453400-18456800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:18453400-18457400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:18454200-18456800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:18454200-18456800	Weak transcription	NHDF-Ad	bronchial
9	chr9:18455800-18456000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:18455800-18458000	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links