Variant report

Variant	rs6569074
Chromosome Location	chr6:119671858-119671859
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	chr6:119670226-119672078	GM12878	blood:	n/a	n/a
2	STAT3	chr6:119671495-119671948	MCF10A-Er-Src	breast:	n/a	n/a
3	MAFF	chr6:119671677-119671956	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:119668645-119672011	GM18505	blood:	n/a	n/a
5	CTCF	chr6:119671840-119671990	HRE	kidney:	n/a	n/a
6	CHD2	chr6:119670515-119671991	GM12878	blood:	n/a	chr6:119671060-119671070 chr6:119671143-119671153
7	BATF	chr6:119671429-119671881	GM12878	blood:	n/a	n/a
8	EP300	chr6:119670750-119671947	GM12878	blood:	n/a	chr6:119671847-119671855 chr6:119671189-119671205
9	CTCF	chr6:119671840-119671990	HRPEpiC	eye:	n/a	n/a
10	NFATC1	chr6:119671342-119672067	GM12878	blood:	n/a	n/a
11	EBF1	chr6:119671458-119671995	GM12878	blood:	n/a	n/a
12	RUNX3	chr6:119671392-119672175	GM12878	blood:	n/a	n/a
13	MTA3	chr6:119670171-119672498	GM12878	blood:	n/a	n/a
14	ZNF143	chr6:119671711-119671906	K562	blood:	n/a	n/a
15	CEBPB	chr6:119671699-119671988	MCF-7	breast:	n/a	n/a
16	IRF1	chr6:119670460-119672556	K562	blood:	n/a	chr6:119671026-119671040 chr6:119671674-119671688 chr6:119671673-119671685 chr6:119672317-119672331 chr6:119671673-119671685
17	NFATC1	chr6:119671282-119672574	GM12878	blood:	n/a	n/a
18	FOS	chr6:119671639-119671913	MCF10A-Er-Src	breast:	n/a	n/a
19	CTCF	chr6:119671800-119671950	AG09319	gingival:	n/a	n/a
20	POLR2A	chr6:119669644-119671953	K562	blood:	n/a	n/a
21	RAD21	chr6:119671480-119672616	HCT-116	colon:	n/a	chr6:119672267-119672286
22	CHD1	chr6:119670735-119672402	GM12878	blood:	n/a	chr6:119671060-119671070 chr6:119671143-119671153
23	POLR2A	chr6:119670176-119671899	K562	blood:	n/a	n/a
24	BHLHE40	chr6:119670357-119672411	GM12878	blood:	n/a	n/a
25	STAT3	chr6:119671548-119672200	MCF10A-Er-Src	breast:	n/a	chr6:119671945-119671957
26	IRF1	chr6:119671502-119672514	K562	blood:	n/a	chr6:119671674-119671688 chr6:119671673-119671685 chr6:119672317-119672331 chr6:119671673-119671685
27	SMC3	chr6:119671498-119672517	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:119669134-119671915	GM12892	blood:	n/a	n/a
29	EP300	chr6:119671494-119671924	GM12878	blood:	n/a	chr6:119671847-119671855
30	SMC3	chr6:119671775-119672453	K562	blood:	n/a	n/a
31	FOXM1	chr6:119671397-119672500	GM12878	blood:	n/a	n/a
32	TEAD4	chr6:119671509-119672477	K562	blood:	n/a	n/a
33	POLR2A	chr6:119668565-119672067	GM19193	blood:	n/a	n/a
34	CEBPB	chr6:119671659-119672010	K562	blood:	n/a	n/a
35	BATF	chr6:119671493-119671883	GM12878	blood:	n/a	n/a
36	STAT5A	chr6:119671395-119672033	GM12878	blood:	n/a	chr6:119671945-119671957
37	EP300	chr6:119671713-119672459	K562	blood:	n/a	chr6:119671847-119671855
38	MAFK	chr6:119671694-119671901	K562	blood:	n/a	n/a
39	MAFK	chr6:119671580-119671960	HepG2	liver:	n/a	n/a
40	SIN3A	chr6:119669529-119671982	H1-hESC	embryonic stem cell:	n/a	chr6:119670299-119670310 chr6:119670397-119670410 chr6:119670262-119670273
41	ARID3A	chr6:119671696-119672498	HepG2	liver:	n/a	n/a
42	POLR2A	chr6:119671282-119672076	GM12878	blood:	n/a	n/a
43	ATF2	chr6:119671419-119672459	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:119671380-119671954	GM12891	blood:	n/a	n/a
45	FOS	chr6:119671625-119671895	MCF10A-Er-Src	breast:	n/a	n/a
46	CTCF	chr6:119670364-119672561	SK-N-SH	brain:	n/a	chr6:119670437-119670450 chr6:119672266-119672284
47	STAT1	chr6:119671318-119671926	GM12878	blood:	n/a	chr6:119671371-119671383
48	MAX	chr6:119670469-119671925	GM12878	blood:	n/a	chr6:119671385-119671395
49	MAZ	chr6:119670490-119671912	GM12878	blood:	n/a	chr6:119671385-119671395
50	POLR2A	chr6:119670492-119671913	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:119467858..119470789-chr6:119668770..119672252,3	K562	blood:
2	chr1:11779444..11779992-chr6:119671388..119671888,2	NB4	blood:
3	chr6:119669555..119672250-chr9:133998872..134001645,2	MCF-7	breast:
4	chr6:119671114..119672646-chr6:119674979..119676830,2	K562	blood:
5	chr6:119671503..119673094-chr6:120039219..120042156,2	K562	blood:
6	chr6:119671114..119673053-chr6:119674972..119676830,3	K562	blood:
7	chr6:119671568..119672634-chr6:120040996..120041889,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASF1A-6	chr6:119671256-119673798	NONHSAT114714

Variant related genes	Relation type
MAN1A1	TF binding region
ENSG00000126883	Chromatin interaction
ENSG00000111879	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1104741	0.83[EUR][1000 genomes]
rs11153802	0.83[EUR][1000 genomes]
rs11153813	0.86[ASN][1000 genomes]
rs11962211	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12211868	0.83[EUR][1000 genomes]
rs1295379	0.86[ASN][1000 genomes]
rs1295386	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1295390	0.86[ASN][1000 genomes]
rs1295392	0.91[YRI][hapmap]
rs1298630	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1342316	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1408492	0.83[EUR][1000 genomes]
rs1408493	0.81[EUR][1000 genomes]
rs1797064	0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs195046	0.81[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs195051	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs195062	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs195063	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs195071	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs195076	0.85[ASN][1000 genomes]
rs195078	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs195079	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs195081	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs195083	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs195086	0.86[ASN][1000 genomes]
rs195088	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs195091	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs195092	0.86[YRI][hapmap]
rs2180040	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2357164	0.87[YRI][hapmap]
rs3778111	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs4945633	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4946406	0.87[YRI][hapmap]
rs4946409	0.88[ASN][1000 genomes]
rs4946428	0.80[JPT][hapmap]
rs6569063	0.81[ASN][1000 genomes]
rs6569075	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6921356	0.92[ASN][1000 genomes]
rs6924723	0.90[ASN][1000 genomes]
rs6937640	0.81[AFR][1000 genomes]
rs7765368	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs7773367	0.92[ASN][1000 genomes]
rs9320684	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9372527	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9374791	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9374801	0.80[JPT][hapmap]
rs9387646	0.83[ASN][1000 genomes]
rs9398510	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9489633	0.81[EUR][1000 genomes]
rs9489654	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv1802628	chr6:119647135-119678881	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119664800-119672400	Active TSS	Brain Anterior Caudate	brain
2	chr6:119665200-119672800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:119666200-119672600	Active TSS	NHDF-Ad	bronchial
4	chr6:119666600-119672400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr6:119667000-119672400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:119667000-119672400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:119667000-119672800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:119667200-119672200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:119667200-119672400	Active TSS	Right Atrium	heart
10	chr6:119667600-119672000	Active TSS	Lung	lung
11	chr6:119667600-119672000	Active TSS	Pancreas	Pancrea
12	chr6:119667600-119672200	Active TSS	Brain Angular Gyrus	brain
13	chr6:119667600-119672200	Active TSS	Left Ventricle	heart
14	chr6:119667600-119672200	Active TSS	Rectal Smooth Muscle	rectum
15	chr6:119667800-119672200	Active TSS	Right Ventricle	heart
16	chr6:119668000-119672000	Active TSS	Gastric	stomach
17	chr6:119668000-119672200	Active TSS	Psoas Muscle	Psoas
18	chr6:119668200-119672000	Active TSS	Aorta	Aorta
19	chr6:119668200-119672000	Active TSS	Fetal Intestine Large	intestine
20	chr6:119668200-119672200	Active TSS	Fetal Intestine Small	intestine
21	chr6:119668200-119672600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:119668200-119672600	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr6:119668400-119672000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:119668400-119672200	Active TSS	Colon Smooth Muscle	Colon
25	chr6:119668400-119672200	Active TSS	Stomach Mucosa	stomach
26	chr6:119668600-119672200	Active TSS	Duodenum Mucosa	Duodenum
27	chr6:119668800-119672000	Active TSS	Ovary	ovary
28	chr6:119668800-119672000	Active TSS	Small Intestine	intestine
29	chr6:119668800-119672200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:119669000-119672000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr6:119669000-119672000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:119669000-119672000	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr6:119669000-119672200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:119669000-119672400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:119669000-119672400	Active TSS	Placenta Amnion	Placenta Amnion
36	chr6:119669200-119672000	Bivalent/Poised TSS	Fetal Brain Female	brain
37	chr6:119669200-119672200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
38	chr6:119669200-119672200	Active TSS	Brain Substantia Nigra	brain
39	chr6:119669400-119672000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
40	chr6:119669400-119672000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:119669400-119672000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
42	chr6:119669400-119672200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr6:119669400-119672200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr6:119669400-119672200	Active TSS	Osteobl	bone
45	chr6:119669400-119672400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr6:119669400-119672400	Active TSS	Stomach Smooth Muscle	stomach
47	chr6:119669400-119673000	Active TSS	GM12878-XiMat	blood
48	chr6:119669600-119672000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:119669600-119672000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:119669600-119672000	Active TSS	Esophagus	oesophagus

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