Variant report

Variant	rs2200870
Chromosome Location	chr6:27832718-27832719
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	YY1	chr6:27831980-27832883	GM12878	blood:	n/a	n/a
2	YY1	chr6:27832610-27832820	K562	blood:	n/a	n/a
3	POU2F2	chr6:27832608-27833646	GM12891	blood:	n/a	chr6:27832881-27832903 chr6:27832888-27832896 chr6:27832886-27832899 chr6:27832887-27832899 chr6:27832889-27832896 chr6:27832886-27832897 chr6:27832888-27832897 chr6:27832888-27832898 chr6:27832887-27832897 chr6:27832888-27832898 chr6:27832883-27832901 chr6:27832885-27832900
4	POLR2A	chr6:27831639-27835944	MCF-7	breast:	n/a	n/a
5	NFIC	chr6:27832621-27835576	GM12878	blood:	n/a	n/a
6	TAF7	chr6:27832651-27836396	H1-hESC	embryonic stem cell:	n/a	n/a
7	TAF1	chr6:27832610-27833412	K562	blood:	n/a	n/a
8	POLR2A	chr6:27831681-27835663	MCF-7	breast:	n/a	n/a
9	YY1	chr6:27832274-27832754	GM12892	blood:	n/a	n/a
10	YY1	chr6:27832244-27832813	GM12891	blood:	n/a	n/a
11	STAT5A	chr6:27832583-27835747	GM12878	blood:	n/a	chr6:27835602-27835610
12	TAF1	chr6:27832629-27833613	H1-hESC	embryonic stem cell:	n/a	n/a
13	CREB1	chr6:27832645-27833241	K562	blood:	n/a	chr6:27832939-27832952
14	POLR2A	chr6:27832618-27835481	GM12891	blood:	n/a	n/a
15	POU2F2	chr6:27832639-27833278	GM12878	blood:	n/a	chr6:27832881-27832903 chr6:27832888-27832896 chr6:27832886-27832899 chr6:27832887-27832899 chr6:27832889-27832896 chr6:27832886-27832897 chr6:27832888-27832897 chr6:27832888-27832898 chr6:27832887-27832897 chr6:27832888-27832898 chr6:27832883-27832901 chr6:27832885-27832900
16	FOXM1	chr6:27832627-27835722	GM12878	blood:	n/a	n/a
17	POU2F2	chr6:27832398-27833638	GM12891	blood:	n/a	chr6:27832881-27832903 chr6:27832888-27832896 chr6:27832886-27832899 chr6:27832887-27832899 chr6:27832889-27832896 chr6:27832886-27832897 chr6:27832888-27832897 chr6:27832888-27832898 chr6:27832887-27832897 chr6:27832888-27832898 chr6:27832883-27832901 chr6:27832885-27832900
18	CEBPB	chr6:27832582-27833164	MCF-7	breast:	n/a	n/a
19	POLR2A	chr6:27832669-27835567	MCF10A-Er-Src	breast:	n/a	n/a
20	HEY1	chr6:27832629-27835529	K562	blood:	n/a	chr6:27832940-27832949 chr6:27832942-27832951
21	POLR2A	chr6:27832608-27835555	GM15510	blood:	n/a	n/a
22	POLR2A	chr6:27832596-27833709	K562	blood:	n/a	n/a
23	POLR2A	chr6:27832654-27835691	SK-N-MC	brain:	n/a	n/a
24	SP1	chr6:27832701-27833271	A549	lung:	n/a	n/a
25	TAF1	chr6:27832560-27833393	GM12878	blood:	n/a	n/a
26	CREB1	chr6:27832563-27833291	GM12878	blood:	n/a	chr6:27832939-27832952
27	POLR2A	chr6:27832605-27835544	GM12878	blood:	n/a	n/a
28	ATF2	chr6:27832684-27835681	H1-hESC	embryonic stem cell:	n/a	n/a
29	PAX5	chr6:27832656-27835467	GM12878	blood:	n/a	chr6:27833102-27833111
30	POLR2A	chr6:27832620-27835499	GM12892	blood:	n/a	n/a
31	YY1	chr6:27832179-27832850	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:27832537-27835575	GM12892	blood:	n/a	n/a
33	RELA	chr6:27832621-27835665	GM18505	blood:	n/a	n/a
34	POLR2A	chr6:27832540-27835501	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:27832483-27835651	GM12892	blood:	n/a	n/a
36	POLR2A	chr6:27832479-27835684	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:27832675-27835716	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr6:27831846-27835556	GM18526	blood:	n/a	n/a
39	CHD1	chr6:27832173-27835389	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:27832667-27835584	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr6:27831541-27835704	PBDE	blood:	n/a	n/a
42	POLR2A	chr6:27832617-27835595	SK-N-SH	brain:	n/a	n/a
43	CREB1	chr6:27832700-27833333	H1-hESC	embryonic stem cell:	n/a	chr6:27832939-27832952
44	SIN3AK20	chr6:27832583-27835816	MCF-7	breast:	n/a	n/a
45	POLR2A	chr6:27832217-27835503	HL-60	blood:	n/a	n/a
46	CREB1	chr6:27832596-27833288	HepG2	liver:	n/a	chr6:27832939-27832952
47	HEY1	chr6:27832533-27835584	K562	blood:	n/a	chr6:27832940-27832949 chr6:27832942-27832951
48	POLR2A	chr6:27832546-27835706	HUVEC	blood vessel:	n/a	n/a
49	RELA	chr6:27832695-27835444	GM12878	blood:	n/a	n/a
50	EBF1	chr6:27832438-27833062	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:27832401..27835225-chr6:159419818..159422166,2	MCF-7	breast:
2	chr6:26154866..26157028-chr6:27832028..27836151,3	MCF-7	breast:
3	chr6:27100613..27102138-chr6:27831418..27834082,2	K562	blood:
4	chr6:26249129..26252003-chr6:27832611..27836378,6	MCF-7	breast:
5	chr6:27100626..27101224-chr6:27832642..27833254,3	Hela-S3	cervix:
6	chr6:27105570..27109142-chr6:27832678..27836176,3	K562	blood:
7	chr6:26215814..26218576-chr6:27831262..27835058,4	K562	blood:
8	chr6:27832024..27834412-chr6:44214386..44216392,2	MCF-7	breast:
9	chr6:27115160..27117823-chr6:27831838..27833565,2	MCF-7	breast:
10	chr6:27832606..27835088-chr6:28302807..28304572,2	K562	blood:
11	chr17:56707936..56710461-chr6:27831380..27834313,2	MCF-7	breast:
12	chr6:27831507..27834483-chr6:28890233..28891763,2	MCF-7	breast:
13	chr6:27113113..27117592-chr6:27831181..27837403,7	MCF-7	breast:
14	chr6:27832219..27835088-chr6:28302807..28305055,2	K562	blood:

Variant related genes	Relation type
HIST1H2BPS2	TF binding region
HIST1H2AL	TF binding region
ENSG00000265565	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000256316	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000271913	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000130363	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12111051	1.00[EUR][1000 genomes]
rs149854	1.00[EUR][1000 genomes]
rs149879	1.00[EUR][1000 genomes]
rs149898	1.00[EUR][1000 genomes]
rs156741	1.00[EUR][1000 genomes]
rs156742	1.00[EUR][1000 genomes]
rs16867899	1.00[EUR][1000 genomes]
rs16867901	1.00[EUR][1000 genomes]
rs169263	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs175953	1.00[EUR][1000 genomes]
rs175955	1.00[EUR][1000 genomes]
rs183926	1.00[EUR][1000 genomes]
rs187995	0.83[AMR][1000 genomes]
rs200959	0.83[AMR][1000 genomes]
rs200962	1.00[EUR][1000 genomes]
rs200970	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs203867	1.00[EUR][1000 genomes]
rs203874	1.00[EUR][1000 genomes]
rs276366	1.00[EUR][1000 genomes]
rs276367	1.00[EUR][1000 genomes]
rs276368	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs276372	1.00[EUR][1000 genomes]
rs425159	1.00[EUR][1000 genomes]
rs55965630	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56221999	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56262840	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56366090	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58700542	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60554811	1.00[EUR][1000 genomes]
rs61275289	1.00[AMR][1000 genomes]
rs73739606	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73739685	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73739773	1.00[AMR][1000 genomes]
rs73740805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73742455	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839777	1.00[EUR][1000 genomes]
rs9295739	1.00[EUR][1000 genomes]
rs9461396	1.00[EUR][1000 genomes]
rs9468189	1.00[EUR][1000 genomes]
rs9468190	1.00[EUR][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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases
7	nsv965699	chr6:27831604-27833574	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	32 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27830800-27835800	Active TSS	K562	blood
2	chr6:27831200-27832800	Weak transcription	HepG2	liver
3	chr6:27831200-27835800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:27831200-27835800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:27831400-27833000	Weak transcription	Hela-S3	cervix
6	chr6:27831400-27833800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
7	chr6:27831400-27834400	Active TSS	NHDF-Ad	bronchial
8	chr6:27831400-27835600	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:27831600-27832800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:27831600-27833400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:27831600-27833400	Active TSS	Fetal Intestine Small	intestine
12	chr6:27831600-27835400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr6:27831600-27835600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr6:27831600-27835800	Active TSS	Fetal Kidney	kidney
15	chr6:27831800-27832800	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr6:27831800-27832800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
17	chr6:27831800-27832800	Flanking Active TSS	Placenta	Placenta
18	chr6:27831800-27832800	Flanking Active TSS	Fetal Thymus	thymus
19	chr6:27831800-27833000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
20	chr6:27831800-27833200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
21	chr6:27831800-27833200	Active TSS	Fetal Brain Female	brain
22	chr6:27831800-27833400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:27831800-27833400	Active TSS	Muscle Satellite Cultured Cells	--
24	chr6:27831800-27833400	Active TSS	Fetal Lung	lung
25	chr6:27831800-27833600	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr6:27831800-27833800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:27831800-27833800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
28	chr6:27831800-27834400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:27831800-27834400	Active TSS	Brain Substantia Nigra	brain
30	chr6:27831800-27834400	Active TSS	Fetal Intestine Large	intestine
31	chr6:27831800-27835400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:27831800-27835400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:27831800-27835400	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr6:27831800-27835400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:27831800-27835400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:27831800-27835600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr6:27831800-27835600	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr6:27831800-27835800	Active TSS	Aorta	Aorta
39	chr6:27832000-27832800	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr6:27832000-27832800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr6:27832000-27832800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr6:27832000-27832800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr6:27832000-27833000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:27832000-27833000	Active TSS	Right Atrium	heart
45	chr6:27832000-27833200	Active TSS	HSMM	muscle
46	chr6:27832000-27833200	Active TSS	Osteobl	bone
47	chr6:27832000-27833400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:27832000-27833400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr6:27832000-27833400	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr6:27832000-27833400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain

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