Variant report

Variant	rs558878549
Chromosome Location	chr6:27100072-27100073
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	E2F4	chr6:27099575-27101836	K562	blood:	n/a	chr6:27100770-27100781 chr6:27100767-27100782 chr6:27100769-27100786 chr6:27100771-27100780 chr6:27100772-27100779 chr6:27100772-27100783 chr6:27100772-27100779 chr6:27100772-27100779 chr6:27100769-27100786 chr6:27100771-27100779 chr6:27099754-27099763 chr6:27100772-27100783 chr6:27100772-27100783 chr6:27100768-27100782 chr6:27100880-27100892 chr6:27099714-27099721
2	POLR2A	chr6:27098755-27102444	GM12892	blood:	n/a	n/a
3	FOXA1	chr6:27099987-27100228	T-47D	breast:	n/a	n/a
4	POU2F2	chr6:27099488-27101967	GM12878	blood:	n/a	chr6:27100612-27100624 chr6:27100613-27100621 chr6:27100613-27100622 chr6:27099862-27099873 chr6:27100614-27100621 chr6:27100606-27100627 chr6:27100610-27100625 chr6:27100606-27100628 chr6:27100611-27100624 chr6:27100613-27100623 chr6:27100608-27100626 chr6:27100611-27100622 chr6:27100613-27100623 chr6:27100612-27100622 chr6:27100610-27100624
5	ATF3	chr6:27099561-27101048	A549	lung:	n/a	chr6:27100666-27100679 chr6:27100665-27100678
6	POLR2A	chr6:27099471-27102442	MCF10A-Er-Src	breast:	n/a	n/a
7	SIN3AK20	chr6:27099415-27102067	HCT-116	colon:	n/a	n/a
8	CHD1	chr6:27099141-27102382	H1-hESC	embryonic stem cell:	n/a	n/a
9	NFIC	chr6:27099344-27101224	SK-N-SH	brain:	n/a	chr6:27099820-27099837 chr6:27099820-27099836
10	SMC3	chr6:27099990-27101932	GM12878	blood:	n/a	n/a
11	CTCF	chr6:27099980-27100130	HPAF	blood vessel:	n/a	n/a
12	CEBPB	chr6:27099653-27102745	Hela-S3	cervix:	n/a	chr6:27102346-27102357
13	TCF12	chr6:27099094-27102549	A549	lung:	n/a	n/a
14	ELF1	chr6:27099007-27100201	HCT-116	colon:	n/a	chr6:27099737-27099750
15	SMARCB1	chr6:27099251-27101942	Hela-S3	cervix:	n/a	n/a
16	GABPA	chr6:27099270-27100244	MCF-7	breast:	n/a	n/a
17	POLR2A	chr6:27099465-27101926	HepG2	liver:	n/a	n/a
18	POLR2A	chr6:27099422-27101795	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr6:27099960-27100678	HepG2	liver:	n/a	n/a
20	POLR2A	chr6:27099502-27101973	PFSK-1	brain:	n/a	n/a
21	RUNX3	chr6:27099111-27102037	GM12878	blood:	n/a	chr6:27100819-27100828
22	POLR2A	chr6:27099203-27101989	U87	brain:	n/a	n/a
23	MAX	chr6:27099445-27102587	A549	lung:	n/a	chr6:27100610-27100619
24	NR2C2	chr6:27099728-27101553	HepG2	liver:	n/a	n/a
25	POLR2A	chr6:27098864-27102290	GM19099	blood:	n/a	n/a
26	NFIC	chr6:27099573-27101054	HepG2	liver:	n/a	chr6:27099820-27099837 chr6:27099820-27099836
27	SP4	chr6:27099489-27102080	H1-hESC	embryonic stem cell:	n/a	chr6:27099774-27099785
28	MAX	chr6:27099601-27101372	K562	blood:	n/a	chr6:27100610-27100619
29	POLR2A	chr6:27099592-27102057	HepG2	liver:	n/a	n/a
30	EGR1	chr6:27099564-27100652	K562	blood:	n/a	n/a
31	SETDB1	chr6:27099722-27101029	U2OS	brain:	n/a	n/a
32	MAX	chr6:27098859-27101965	Hela-S3	cervix:	n/a	chr6:27100610-27100619
33	POLR2A	chr6:27098707-27102455	GM12878	blood:	n/a	n/a
34	SIN3A	chr6:27099465-27102013	GM12878	blood:	n/a	n/a
35	PML	chr6:27099393-27102534	K562	blood:	n/a	n/a
36	ZBTB33	chr6:27099998-27100629	GM12878	blood:	n/a	n/a
37	JUND	chr6:27099599-27101288	K562	blood:	n/a	chr6:27100646-27100655
38	POLR2A	chr6:27099312-27102055	MCF-7	breast:	n/a	n/a
39	POLR2A	chr6:27099098-27102095	HL-60	blood:	n/a	n/a
40	POLR2A	chr6:27098802-27102692	K562	blood:	n/a	n/a
41	POLR2A	chr6:27099492-27101916	HCT-116	colon:	n/a	n/a
42	POLR2A	chr6:27098515-27102749	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr6:27098735-27102399	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:27099245-27101942	GM19193	blood:	n/a	n/a
45	CTCF	chr6:27100000-27100150	HUVEC	blood vessel:	n/a	n/a
46	BCLAF1	chr6:27099081-27102104	GM12878	blood:	n/a	n/a
47	ATF2	chr6:27099400-27102439	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr6:27100040-27100190	HEK293	kidney:	n/a	n/a
49	POLR2A	chr6:27099499-27102126	GM12878	blood:	n/a	n/a
50	SP1	chr6:27099991-27101309	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26283553..26287733-chr6:27097522..27103890,12	K562	blood:
2	chr22:19466508..19469861-chr6:27098397..27102298,3	K562	blood:
3	chr6:26156157..26159561-chr6:27098059..27103137,9	MCF-7	breast:
4	chr12:123717412..123717915-chr6:27099859..27100533,2	Hela-S3	cervix:
5	chr6:27096288..27105112-chr6:27855525..27865082,32	K562	blood:
6	chr6:26187507..26190261-chr6:27099153..27102365,6	MCF-7	breast:
7	chr6:26214809..26219329-chr6:27098036..27102129,6	MCF-7	breast:
8	chr6:27094403..27106138-chr6:27772392..27783072,46	MCF-7	breast:
9	chr6:26210558..26220469-chr6:27093552..27103796,28	K562	blood:
10	chr3:64006479..64009154-chr6:27099911..27101593,2	MCF-7	breast:
11	chr6:26519250..26523737-chr6:27099178..27105777,8	K562	blood:
12	chr6:26233448..26235462-chr6:27099272..27101626,2	MCF-7	breast:
13	chr6:26155271..26161648-chr6:27095163..27104437,21	K562	blood:
14	chr6:26023233..26029617-chr6:27098032..27102736,8	MCF-7	breast:
15	chr6:26121882..26125935-chr6:27097712..27102367,10	MCF-7	breast:
16	chr11:62389082..62389744-chr6:27099706..27100681,2	Hela-S3	cervix:
17	chr6:26196890..26209578-chr6:27096615..27108451,46	K562	blood:
18	chr6:27094943..27118570-chr6:27854106..27868030,101	K562	blood:
19	chr6:27099529..27101818-chr6:27857109..27860986,3	MCF-7	breast:
20	chr3:170586359..170588667-chr6:27099127..27101405,2	K562	blood:
21	chr6:27098287..27101143-chr6:27833943..27835585,2	MCF-7	breast:
22	chr6:26986141..26989315-chr6:27099693..27102722,3	K562	blood:
23	chr6:27098287..27103463-chr6:27796109..27800380,7	K562	blood:
24	chr6:26031624..26033996-chr6:27097636..27100221,2	MCF-7	breast:
25	chr6:26248241..26251766-chr6:27097726..27103043,5	MCF-7	breast:
26	chr16:69373250..69373872-chr6:27099961..27100820,2	Hela-S3	cervix:
27	chr6:27098129..27102708-chr6:27857691..27863156,15	MCF-7	breast:
28	chr6:26224357..26226740-chr6:27098650..27100322,2	K562	blood:
29	chr6:26231234..26236589-chr6:27099738..27104932,8	K562	blood:
30	chr6:26270978..26274693-chr6:27098356..27103484,7	MCF-7	breast:
31	chr6:26026115..26036040-chr6:27097153..27104835,26	K562	blood:
32	chr6:26187257..26192079-chr6:27098954..27103250,7	MCF-7	breast:
33	chr6:26024161..26035534-chr6:27093020..27104638,25	K562	blood:
34	chr6:26213328..26219374-chr6:27098401..27104203,12	MCF-7	breast:
35	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
36	chr6:27098876..27101009-chr6:27528408..27531042,2	K562	blood:
37	chr6:27098188..27105257-chr6:27800590..27808222,20	K562	blood:
38	chr6:26092213..26093829-chr6:27098200..27100194,2	K562	blood:
39	chr2:28113276..28113924-chr6:27100052..27100806,2	Hela-S3	cervix:
40	chr6:26155265..26160650-chr6:27098824..27104648,17	MCF-7	breast:
41	chr2:114648161..114648926-chr6:27099888..27100517,2	Hela-S3	cervix:
42	chr6:26215032..26220721-chr6:27098305..27106549,21	K562	blood:
43	chr6:26196435..26200575-chr6:27099094..27104350,6	MCF-7	breast:
44	chr6:26119257..26128074-chr6:27097161..27104707,27	K562	blood:
45	chr6:26203350..26205090-chr6:27099738..27102062,2	MCF-7	breast:
46	chr6:26032382..26034370-chr6:27099704..27101484,2	MCF-7	breast:
47	chr22:18111598..18112592-chr6:27099893..27100597,2	Hela-S3	cervix:
48	chr6:26269718..26276565-chr6:27099393..27105112,10	MCF-7	breast:
49	chr6:26283553..26288411-chr6:27099109..27103890,9	K562	blood:
50	chr5:10249652..10251055-chr6:27099838..27101365,4	Hela-S3	cervix:

Variant related genes	Relation type
HIST1H2AG	TF binding region
ENSG00000099968	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000199289	Chromatin interaction
ENSG00000124575	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000099622	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000184357	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000182611	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000168575	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000200463	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000185686	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000136986	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000163584	Chromatin interaction
ENSG00000176209	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000182572	Chromatin interaction
ENSG00000119335	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000224843	Chromatin interaction
ENSG00000218281	Chromatin interaction
ENSG00000238621	Chromatin interaction
ENSG00000150756	Chromatin interaction
ENSG00000218690	Chromatin interaction
ENSG00000168242	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000197914	Chromatin interaction
ENSG00000070010	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000127947	Chromatin interaction
ENSG00000115091	Chromatin interaction
ENSG00000256316	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000197238	Chromatin interaction
ENSG00000213380	Chromatin interaction
ENSG00000132603	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000188987	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000187239	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000216331	Chromatin interaction
ENSG00000217275	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000010704	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000156787	Chromatin interaction
ENSG00000197061	Chromatin interaction
ENSG00000093009	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000219738	Chromatin interaction
ENSG00000171174	Chromatin interaction
ENSG00000150753	Chromatin interaction
ENSG00000163636	Chromatin interaction
ENSG00000256018	Chromatin interaction
ENSG00000196966	Chromatin interaction
ENSG00000158019	Chromatin interaction
ENSG00000238610	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1029124	chr6:26825468-27109774	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	244 gene(s)	inside rSNPs	diseases
3	nsv965698	chr6:27099698-27100316	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	102 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27098000-27102200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:27098200-27101800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr6:27098400-27100600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:27098400-27101600	Active TSS	GM12878-XiMat	blood
5	chr6:27098400-27102400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:27098400-27102400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:27098400-27102800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:27098600-27101000	Active TSS	HMEC	breast
9	chr6:27098600-27102000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:27098600-27102200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:27098600-27102400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr6:27098600-27102400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:27098800-27100200	Active TSS	Brain Anterior Caudate	brain
14	chr6:27098800-27101600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:27098800-27101800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:27098800-27101800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:27098800-27102000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:27098800-27102000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:27098800-27102200	Active TSS	Brain Germinal Matrix	brain
20	chr6:27098800-27102400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr6:27098800-27102400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:27098800-27102400	Active TSS	Fetal Kidney	kidney
23	chr6:27098800-27102400	Active TSS	NHLF	lung
24	chr6:27098800-27102800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:27098800-27102800	Active TSS	A549	lung
26	chr6:27098800-27104600	Active TSS	K562	blood
27	chr6:27099000-27100200	Active TSS	Aorta	Aorta
28	chr6:27099000-27100800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:27099000-27100800	Active TSS	Colonic Mucosa	Colon
30	chr6:27099000-27100800	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr6:27099000-27101000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:27099000-27101000	Active TSS	Muscle Satellite Cultured Cells	--
33	chr6:27099000-27101200	Active TSS	Fetal Brain Male	brain
34	chr6:27099000-27101400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:27099000-27101600	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:27099000-27101600	Active TSS	Fetal Intestine Large	intestine
37	chr6:27099000-27101600	Active TSS	Psoas Muscle	Psoas
38	chr6:27099000-27101600	Active TSS	HSMMtube	muscle
39	chr6:27099000-27101800	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr6:27099000-27101800	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr6:27099000-27102000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:27099000-27102000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:27099000-27102000	Active TSS	Right Ventricle	heart
44	chr6:27099000-27102200	Active TSS	NHDF-Ad	bronchial
45	chr6:27099000-27102400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr6:27099000-27102400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:27099000-27102400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr6:27099200-27100200	Active TSS	Brain Angular Gyrus	brain
49	chr6:27099200-27100200	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr6:27099200-27100200	Active TSS	Lung	lung

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