Variant report

Variant	rs6475220
Chromosome Location	chr9:18469700-18469701
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr9:18469618-18469962	HEK293	kidney:	n/a	n/a
2	SETDB1	chr9:18469658-18469992	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
ADAMTSL1	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1006022	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10123481	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10217753	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs10453192	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10733354	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10738511	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10756965	0.88[AFR][1000 genomes]
rs10756966	0.87[AFR][1000 genomes]
rs10756967	0.91[AFR][1000 genomes]
rs10810972	0.83[ASN][1000 genomes]
rs10810973	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10810974	0.88[CHD][hapmap]
rs10963613	0.82[CEU][hapmap]
rs11793923	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1281352	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1329720	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1340039	0.91[EUR][1000 genomes]
rs1341063	0.86[CHB][hapmap]
rs1417035	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1417037	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1538999	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs16936745	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[AFR][1000 genomes]
rs16936779	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1832638	0.81[EUR][1000 genomes]
rs1888067	0.86[CHB][hapmap]
rs1888068	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1888069	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2149875	0.92[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2153415	0.92[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2153416	0.92[CEU][hapmap];0.80[CHD][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2277160	0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs3898100	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4246142	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4246143	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4590536	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4961651	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4961652	0.92[CEU][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4961653	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4961654	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs6475219	0.95[EUR][1000 genomes]
rs6475221	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7019399	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7032393	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7036515	0.89[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7046502	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7856703	0.81[ASW][hapmap];0.92[CEU][hapmap];0.80[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7864622	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7864727	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7867766	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6475220	FREM1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18464200-18471600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:18464200-18474400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:18464400-18473000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr9:18466400-18471800	Weak transcription	Hela-S3	cervix
5	chr9:18468800-18470200	Weak transcription	Fetal Heart	heart
6	chr9:18469000-18470400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:18469400-18470400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:18469400-18470400	ZNF genes & repeats	NHDF-Ad	bronchial
9	chr9:18469600-18469800	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:18469600-18469800	ZNF genes & repeats	Esophagus	oesophagus

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