Variant report

Variant	rs7656990
Chromosome Location	chr4:119508720-119508721
allele	C/T
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	POLR2A	chr4:119508495-119509034	H1-neurons	neurons:	n/a	n/a
2	SRF	chr4:119508352-119508839	ECC-1	luminal epithelium:	n/a	chr4:119508618-119508632 chr4:119508618-119508635 chr4:119508615-119508632 chr4:119508618-119508629 chr4:119508616-119508631 chr4:119508615-119508633
3	REST	chr4:119508410-119509351	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr4:119508304-119509058	H1-neurons	neurons:	n/a	n/a
5	REST	chr4:119508545-119509053	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119508532..119510926-chr4:119602289..119604089,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260404	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10004322	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022024	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031029	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10857060	1.00[ASN][1000 genomes]
rs11728902	0.83[EUR][1000 genomes]
rs11734153	1.00[ASN][1000 genomes]
rs11945703	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12331454	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12648682	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12648778	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13115157	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13124091	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13137401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146440	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs13146816	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs2029399	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs2046779	0.94[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap]
rs2389780	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2728403	0.85[EUR][1000 genomes]
rs2787191	0.88[EUR][1000 genomes]
rs28448851	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3087958	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs35183273	0.82[EUR][1000 genomes]
rs35890030	0.98[ASN][1000 genomes]
rs3733517	0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4001330	0.87[ASN][1000 genomes]
rs67276048	0.85[EUR][1000 genomes]
rs67655207	0.84[EUR][1000 genomes]
rs6813357	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6821350	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs6833597	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6836005	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs6847706	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs6857285	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs71241793	0.83[EUR][1000 genomes]
rs71610209	0.87[ASN][1000 genomes]
rs72676188	0.96[ASN][1000 genomes]
rs7653962	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7669896	1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs7689541	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692721	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs7695602	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs9760578	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1002771	chr4:119125361-119571237	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv980150	chr4:119499004-119514502	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7656990	RP11-384K6.6	cis	Skin Sun Exposed Lower leg	GTEx
rs7656990	RP11-384K6.6	cis	Esophagus Mucosa	GTEx
rs7656990	RP11-384K6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7656990	RP11-384K6.6	cis	Nerve Tibial	GTEx
rs7656990	RP11-384K6.6	cis	Artery Tibial	GTEx
rs7656990	RP11-384K6.2	cis	Thyroid	GTEx
rs7656990	PRSS12	cis	parietal	SCAN
rs7656990	RP11-384K6.6	cis	Thyroid	GTEx
rs7656990	RP11-384K6.6	cis	Adipose Subcutaneous	GTEx
rs7656990	RP11-384K6.6	cis	Whole Blood	GTEx
rs7656990	RP11-384K6.6	cis	lung	GTEx
rs7656990	RP11-384K6.6	cis	Esophagus Muscularis	GTEx
rs7656990	RP11-384K6.2	cis	Nerve Tibial	GTEx
rs7656990	RP11-384K6.2	cis	Artery Tibial	GTEx
rs7656990	RP11-384K6.2	cis	lung	GTEx
rs7656990	RP11-384K6.2	cis	Whole Blood	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119506600-119512800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:119507200-119512400	Weak transcription	Hela-S3	cervix
3	chr4:119507200-119512600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:119507400-119512200	Weak transcription	Stomach Mucosa	stomach
5	chr4:119507400-119512400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:119507800-119508800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:119507800-119508800	Bivalent Enhancer	Osteobl	bone
8	chr4:119507800-119509000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:119507800-119512000	Weak transcription	Left Ventricle	heart
10	chr4:119507800-119513200	Weak transcription	Spleen	Spleen
11	chr4:119508000-119508800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:119508000-119509000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:119508000-119512000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:119508000-119512000	Weak transcription	Pancreas	Pancrea
15	chr4:119508000-119512000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:119508000-119512200	Weak transcription	K562	blood
17	chr4:119508000-119512400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:119508000-119512400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:119508000-119512400	Weak transcription	Ovary	ovary
20	chr4:119508000-119512600	Weak transcription	HSMM	muscle
21	chr4:119508200-119509400	Enhancers	Liver	Liver
22	chr4:119508200-119512400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:119508600-119512000	Weak transcription	Adipose Nuclei	Adipose

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