Variant report

Variant	rs6840580
Chromosome Location	chr4:129389738-129389739
allele	A/G
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	ARID3A	chr4:129389572-129389842	K562	blood:	n/a	n/a
2	MAX	chr4:129389567-129389939	SK-N-SH	brain:	n/a	chr4:129389754-129389763
3	RCOR1	chr4:129389559-129390049	K562	blood:	n/a	n/a
4	REST	chr4:129389180-129390165	H1-neurons	neurons:	n/a	n/a
5	RAD21	chr4:129389621-129389916	SK-N-SH_RA	brain:	n/a	n/a
6	CEBPB	chr4:129389462-129389898	IMR90	lung:	n/a	n/a
7	USF2	chr4:129389676-129389907	K562	blood:	n/a	chr4:129389752-129389763
8	POLR2A	chr4:129389493-129389890	H1-neurons	neurons:	n/a	n/a
9	USF1	chr4:129389620-129389934	H1-hESC	embryonic stem cell:	n/a	n/a
10	GATA1	chr4:129388586-129390232	PBDE	blood:	n/a	n/a
11	STAT3	chr4:129389657-129389877	MCF10A-Er-Src	breast:	n/a	chr4:129389803-129389814
12	USF1	chr4:129389599-129389929	A549	lung:	n/a	n/a
13	CBX3	chr4:129389507-129389956	K562	blood:	n/a	n/a
14	PBX3	chr4:129389545-129390045	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr4:129389524-129389868	U87	brain:	n/a	n/a
16	POLR2A	chr4:129389455-129389995	U87	brain:	n/a	n/a
17	MAX	chr4:129389622-129390039	K562	blood:	n/a	chr4:129389754-129389763
18	YY1	chr4:129389568-129389929	SK-N-SH_RA	brain:	n/a	n/a
19	IRF1	chr4:129389615-129390027	K562	blood:	n/a	chr4:129389803-129389816 chr4:129389800-129389814 chr4:129389804-129389818 chr4:129389804-129389814 chr4:129389803-129389816 chr4:129389803-129389816 chr4:129389798-129389815 chr4:129389798-129389819 chr4:129389803-129389814
20	MAX	chr4:129389655-129389996	SK-N-SH	brain:	n/a	chr4:129389754-129389763
21	MAFK	chr4:129389614-129389957	K562	blood:	n/a	n/a
22	POLR2A	chr4:129389574-129389830	SK-N-SH	brain:	n/a	n/a
23	FOS	chr4:129389607-129389918	MCF10A-Er-Src	breast:	n/a	n/a
24	USF1	chr4:129389598-129389942	SK-N-SH_RA	brain:	n/a	n/a
25	CUX1	chr4:129389266-129389874	K562	blood:	n/a	n/a
26	USF1	chr4:129389547-129389918	SK-N-SH_RA	brain:	n/a	n/a
27	POLR2A	chr4:129389341-129389824	MCF10A-Er-Src	breast:	n/a	n/a
28	FOS	chr4:129389658-129389928	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr4:129389615-129389939	MCF10A-Er-Src	breast:	n/a	n/a
30	MYC	chr4:129389503-129389918	MCF10A-Er-Src	breast:	n/a	chr4:129389754-129389763
31	USF2	chr4:129389643-129389850	GM12878	blood:	n/a	chr4:129389752-129389763
32	MAX	chr4:129389622-129389861	K562	blood:	n/a	chr4:129389754-129389763
33	EP300	chr4:129389706-129389836	GM12878	blood:	n/a	n/a
34	MYC	chr4:129389670-129389918	MCF10A-Er-Src	breast:	n/a	chr4:129389754-129389763
35	BHLHE40	chr4:129389578-129389928	K562	blood:	n/a	n/a
36	STAT3	chr4:129389693-129389865	MCF10A-Er-Src	breast:	n/a	chr4:129389803-129389814
37	EP300	chr4:129389493-129390154	K562	blood:	n/a	n/a
38	YY1	chr4:129389596-129389881	K562	blood:	n/a	n/a
39	IRF1	chr4:129389570-129390208	K562	blood:	n/a	chr4:129389803-129389816 chr4:129389800-129389814 chr4:129389804-129389818 chr4:129389804-129389814 chr4:129389803-129389816 chr4:129389803-129389816 chr4:129389798-129389815 chr4:129389798-129389819 chr4:129389803-129389814
40	USF2	chr4:129389586-129389941	Hela-S3	cervix:	n/a	chr4:129389752-129389763
41	ATF3	chr4:129389637-129389824	K562	blood:	n/a	chr4:129389754-129389763
42	NFIC	chr4:129389469-129390169	SK-N-SH	brain:	n/a	n/a
43	MAZ	chr4:129389597-129389859	K562	blood:	n/a	chr4:129389754-129389763
44	MYC	chr4:129389627-129389963	K562	blood:	n/a	chr4:129389754-129389763
45	EP300	chr4:129389559-129389911	SK-N-SH_RA	brain:	n/a	n/a
46	SIN3AK20	chr4:129389584-129389904	SK-N-SH	brain:	n/a	n/a
47	STAT3	chr4:129389714-129389914	MCF10A-Er-Src	breast:	n/a	chr4:129389803-129389814
48	POLR2A	chr4:129389535-129389875	IMR90	lung:	n/a	n/a
49	POLR2A	chr4:129389662-129389752	ProgFib	skin:	n/a	n/a
50	POLR2A	chr4:129389491-129389887	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:129375534..129378245-chr4:129388256..129389857,2	MCF-7	breast:
2	chr4:129388958..129391166-chr4:129391336..129393965,2	K562	blood:
3	chr4:129387442..129390283-chr4:129446907..129450145,3	MCF-7	breast:
4	chr4:129389395..129391397-chr4:129484580..129487004,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251432	TF binding region
ENSG00000251432	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11733387	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11937124	0.88[AMR][1000 genomes]
rs13108573	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13115644	0.87[AFR][1000 genomes]
rs17337491	1.00[ASW][hapmap]
rs2062456	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2133465	1.00[ASW][hapmap]
rs3733260	1.00[LWK][hapmap]
rs4305531	1.00[ASW][hapmap]
rs4362840	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4975221	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs6534679	1.00[ASW][hapmap]
rs6534686	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6534687	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6821679	0.88[AMR][1000 genomes]
rs6849290	0.83[CEU][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7441245	1.00[ASW][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129376600-129393200	Weak transcription	Placenta	Placenta
2	chr4:129376600-129406200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:129376600-129435000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:129377000-129397000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:129377600-129394400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:129383000-129389800	Weak transcription	HSMMtube	muscle
7	chr4:129383000-129398800	Weak transcription	Pancreas	Pancrea
8	chr4:129386600-129398200	Weak transcription	Primary T cells from cord blood	blood
9	chr4:129387800-129390400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:129388000-129390000	Enhancers	NHDF-Ad	bronchial
11	chr4:129388200-129389800	Enhancers	Aorta	Aorta
12	chr4:129388400-129390400	Enhancers	Osteobl	bone
13	chr4:129388600-129406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:129388800-129389800	Enhancers	Right Atrium	heart
15	chr4:129388800-129389800	Enhancers	K562	blood
16	chr4:129388800-129390200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:129388800-129390200	Enhancers	Fetal Brain Male	brain
18	chr4:129388800-129390400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr4:129388800-129390400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr4:129389000-129389800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:129389000-129389800	Enhancers	Fetal Brain Female	brain
22	chr4:129389000-129389800	Enhancers	Fetal Muscle Leg	muscle
23	chr4:129389000-129389800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr4:129389000-129390000	Enhancers	Brain Angular Gyrus	brain
25	chr4:129389000-129390000	Enhancers	Rectal Smooth Muscle	rectum
26	chr4:129389000-129390000	Active TSS	Stomach Smooth Muscle	stomach
27	chr4:129389000-129390200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:129389000-129390200	Enhancers	Colon Smooth Muscle	Colon
29	chr4:129389000-129390200	Enhancers	Fetal Heart	heart
30	chr4:129389000-129390400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:129389000-129390400	Enhancers	Adipose Nuclei	Adipose
32	chr4:129389000-129390400	Enhancers	Fetal Lung	lung
33	chr4:129389000-129390400	Enhancers	A549	lung
34	chr4:129389000-129390600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr4:129389200-129389800	Enhancers	Fetal Intestine Small	intestine
36	chr4:129389200-129390000	Weak transcription	Ovary	ovary
37	chr4:129389200-129390200	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr4:129389200-129390200	Enhancers	Fetal Stomach	stomach
39	chr4:129389200-129390400	Enhancers	HSMM	muscle
40	chr4:129389200-129390400	Enhancers	NHLF	lung
41	chr4:129389200-129391400	Weak transcription	Left Ventricle	heart
42	chr4:129389400-129389800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:129389400-129390000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:129389400-129390200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:129389400-129390200	Enhancers	Fetal Intestine Large	intestine
46	chr4:129389600-129389800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:129389600-129389800	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr4:129389600-129390000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr4:129389600-129390000	Active TSS	Brain Anterior Caudate	brain
50	chr4:129389600-129390000	Active TSS	Brain Cingulate Gyrus	brain

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