Variant report

Variant	rs1625691
Chromosome Location	chr4:57845740-57845741
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr4:57844701-57846119	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:57845738-57845929	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:57844607-57846114	GM12878	blood:	n/a	n/a
4	ZNF384	chr4:57845725-57846408	K562	blood:	n/a	n/a
5	POLR2A	chr4:57844666-57846022	GM12892	blood:	n/a	n/a
6	HEY1	chr4:57845681-57846056	K562	blood:	n/a	n/a
7	MXI1	chr4:57842395-57846714	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr4:57843096-57846049	GM12878	blood:	n/a	n/a
9	CHD1	chr4:57844739-57846307	IMR90	lung:	n/a	n/a
10	POLR2A	chr4:57843364-57846151	GM12891	blood:	n/a	n/a
11	POLR2A	chr4:57844650-57846015	K562	blood:	n/a	n/a
12	POLR2A	chr4:57844755-57846012	IMR90	lung:	n/a	n/a
13	MXI1	chr4:57844710-57845947	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:57845686-57846089	K562	blood:	n/a	n/a
15	POLR2A	chr4:57845593-57846150	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:57845701-57846012	K562	blood:	n/a	n/a
17	POLR2A	chr4:57845740-57846036	Hela-S3	cervix:	n/a	n/a
18	JUND	chr4:57845701-57846091	K562	blood:	n/a	n/a
19	POLR2A	chr4:57842909-57846039	Hela-S3	cervix:	n/a	n/a
20	MTA3	chr4:57844527-57846086	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:57843073-57846196	HepG2	liver:	n/a	n/a
22	SIN3AK20	chr4:57845601-57845973	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57301138..57303431-chr4:57844871..57846919,2	MCF-7	breast:
2	chr4:57844609..57846562-chr4:57874022..57876813,2	K562	blood:
3	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:
4	chr4:57822641..57828782-chr4:57838494..57846737,10	K562	blood:
5	chr4:57332287..57335313-chr4:57842375..57846822,5	K562	blood:
6	chr4:57845155..57847188-chr4:57856587..57858696,2	MCF-7	breast:
7	chr4:57772839..57777394-chr4:57841397..57848240,17	K562	blood:
8	chr4:57332264..57334926-chr4:57844078..57846239,2	MCF-7	breast:

No data

Variant related genes	Relation type
NOA1	TF binding region
ENSG00000084093	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000269949	Chromatin interaction
ENSG00000047315	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10866440	1.00[JPT][hapmap]
rs10866441	1.00[JPT][hapmap]
rs1105434	1.00[JPT][hapmap]
rs1107675	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11727683	0.84[ASN][1000 genomes]
rs11730321	0.93[JPT][hapmap]
rs11735158	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11932673	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12500454	1.00[JPT][hapmap]
rs1277271	0.89[ASN][1000 genomes]
rs1277287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1277288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108245	1.00[JPT][hapmap]
rs13121176	0.80[ASN][1000 genomes]
rs1315005	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1315006	0.83[EUR][1000 genomes]
rs17081937	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17087307	0.82[ASN][1000 genomes]
rs17087317	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17087411	0.87[JPT][hapmap]
rs17087414	0.87[JPT][hapmap]
rs1713994	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1713997	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1713998	1.00[ASW][hapmap];0.80[MKK][hapmap]
rs1718837	0.91[CEU][hapmap];0.95[TSI][hapmap]
rs1718839	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1718882	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1718886	0.81[TSI][hapmap]
rs1877669	1.00[JPT][hapmap]
rs1976780	0.82[ASN][1000 genomes]
rs2228991	1.00[JPT][hapmap]
rs3000	1.00[JPT][hapmap]
rs34576794	0.87[ASN][1000 genomes]
rs34659774	0.82[ASN][1000 genomes]
rs3733306	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs3796528	1.00[JPT][hapmap]
rs3806745	1.00[JPT][hapmap]
rs41552420	0.82[ASN][1000 genomes]
rs41556916	0.84[ASN][1000 genomes]
rs56182208	0.84[ASN][1000 genomes]
rs56285301	0.84[ASN][1000 genomes]
rs57469512	0.84[ASN][1000 genomes]
rs6554398	1.00[JPT][hapmap]
rs6816457	0.89[ASN][1000 genomes]
rs6838948	1.00[JPT][hapmap]
rs6847086	0.82[JPT][hapmap]
rs6852110	1.00[JPT][hapmap]
rs708547	0.86[TSI][hapmap]
rs73242624	0.87[EUR][1000 genomes]
rs73242631	0.82[ASN][1000 genomes]
rs7661194	1.00[JPT][hapmap]
rs7680734	1.00[JPT][hapmap]
rs781665	0.88[ASN][1000 genomes]
rs781666	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs781668	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9942208	1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription 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 target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1625691	POLR2B	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57840800-57846800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr4:57841400-57846200	Active TSS	HMEC	breast
3	chr4:57841400-57846200	Active TSS	NHEK	skin
4	chr4:57841400-57846400	Active TSS	GM12878-XiMat	blood
5	chr4:57841400-57846600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:57841400-57846600	Active TSS	Hela-S3	cervix
7	chr4:57841600-57846600	Active TSS	NHLF	lung
8	chr4:57841800-57846400	Active TSS	Fetal Intestine Large	intestine
9	chr4:57842000-57846000	Active TSS	Gastric	stomach
10	chr4:57842000-57846200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:57842000-57846200	Active TSS	H1 Cell Line	embryonic stem cell
12	chr4:57842000-57846200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:57842000-57846200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr4:57842000-57846200	Active TSS	Fetal Kidney	kidney
15	chr4:57842000-57846200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr4:57842000-57846200	Active TSS	Ovary	ovary
17	chr4:57842000-57846400	Active TSS	Fetal Intestine Small	intestine
18	chr4:57842000-57846600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr4:57842000-57846600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr4:57842000-57846600	Active TSS	HSMM	muscle
21	chr4:57842000-57846600	Active TSS	K562	blood
22	chr4:57842000-57846800	Active TSS	HSMMtube	muscle
23	chr4:57842000-57847000	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr4:57842000-57847000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:57842000-57847000	Active TSS	A549	lung
26	chr4:57842200-57846000	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr4:57842200-57846000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:57842200-57846000	Active TSS	Lung	lung
29	chr4:57842200-57846000	Active TSS	Small Intestine	intestine
30	chr4:57842200-57846000	Active TSS	Stomach Mucosa	stomach
31	chr4:57842200-57846600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:57842400-57846000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:57842400-57846200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:57842600-57845800	Active TSS	Colon Smooth Muscle	Colon
35	chr4:57842600-57846000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:57842600-57846000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:57842600-57846000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr4:57842600-57846000	Active TSS	Aorta	Aorta
39	chr4:57842600-57846000	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr4:57842600-57846000	Active TSS	Spleen	Spleen
41	chr4:57842600-57846200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:57842600-57846200	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr4:57842600-57846200	Active TSS	Fetal Lung	lung
44	chr4:57842600-57846200	Active TSS	Osteobl	bone
45	chr4:57842600-57846400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:57842600-57846600	Active TSS	NHDF-Ad	bronchial
47	chr4:57842800-57845800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:57842800-57845800	Active TSS	Brain Angular Gyrus	brain
49	chr4:57842800-57845800	Active TSS	Duodenum Mucosa	Duodenum
50	chr4:57842800-57846000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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