Variant report

Variant	rs2010963
Chromosome Location	chr6:43738350-43738351
allele	C/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	MXI1	chr6:43737221-43738668	Hela-S3	cervix:	n/a	n/a
2	ZNF263	chr6:43737198-43741637	HEK293-T-REx	kidney:	n/a	chr6:43739329-43739338 chr6:43740584-43740593 chr6:43740575-43740584
3	TAF1	chr6:43737506-43738852	K562	blood:	n/a	n/a
4	POLR2A	chr6:43737189-43741402	K562	blood:	n/a	n/a
5	MBD4	chr6:43736836-43738459	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:43738196-43738631	HepG2	liver:	n/a	n/a
7	MAX	chr6:43737244-43738663	Hela-S3	cervix:	n/a	chr6:43737895-43737904
8	TAF1	chr6:43738144-43738486	Hela-S3	cervix:	n/a	n/a
9	JUND	chr6:43738227-43738440	H1-hESC	embryonic stem cell:	n/a	n/a
10	TAF1	chr6:43737588-43740068	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr6:43737122-43741423	K562	blood:	n/a	chr6:43739126-43739135 chr6:43739801-43739811 chr6:43739253-43739262 chr6:43739604-43739614 chr6:43739715-43739724 chr6:43737895-43737904 chr6:43739142-43739151
12	POLR2A	chr6:43736721-43742330	K562	blood:	n/a	n/a
13	TCF7L2	chr6:43736983-43738361	HCT-116	colon:	n/a	chr6:43737140-43737149 chr6:43737137-43737153 chr6:43737141-43737151 chr6:43737137-43737153 chr6:43737141-43737150 chr6:43737138-43737152
14	SIN3A	chr6:43737277-43739838	GM12878	blood:	n/a	chr6:43739074-43739087 chr6:43739497-43739508
15	POLR2A	chr6:43737140-43743129	Hela-S3	cervix:	n/a	n/a
16	HMGN3	chr6:43737338-43739945	K562	blood:	n/a	n/a
17	RAD21	chr6:43736023-43741991	SK-N-SH	brain:	n/a	chr6:43737365-43737384 chr6:43737156-43737175 chr6:43736856-43736866 chr6:43739442-43739454 chr6:43737505-43737515 chr6:43739440-43739453
18	E2F4	chr6:43737224-43739883	K562	blood:	n/a	chr6:43739067-43739077 chr6:43739208-43739217 chr6:43739424-43739436 chr6:43739315-43739327
19	PBX3	chr6:43738175-43738692	SK-N-SH	brain:	n/a	n/a
20	SMC3	chr6:43736561-43743761	SK-N-SH	brain:	n/a	chr6:43739308-43739322 chr6:43737366-43737380 chr6:43737167-43737181
21	TAL1	chr6:43737226-43738682	K562	blood:	n/a	n/a
22	CTCF	chr6:43736587-43738730	SK-N-SH	brain:	n/a	chr6:43737364-43737382 chr6:43737365-43737381 chr6:43737366-43737387 chr6:43737369-43737379
23	POLR2A	chr6:43738193-43738543	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIN3AK20	chr6:43738267-43738827	H1-hESC	embryonic stem cell:	n/a	n/a
25	E2F4	chr6:43737344-43738360	MCF10A-Er-Src	breast:	n/a	n/a
26	IRF1	chr6:43737268-43738490	K562	blood:	n/a	n/a
27	ZBTB7A	chr6:43738203-43739944	K562	blood:	n/a	chr6:43739932-43739939 chr6:43739207-43739216
28	CHD2	chr6:43738274-43738830	H1-hESC	embryonic stem cell:	n/a	n/a
29	MXI1	chr6:43736768-43738465	HepG2	liver:	n/a	n/a
30	POLR2A	chr6:43738242-43739957	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:43737209-43740284	GM12878	blood:	n/a	n/a
32	RCOR1	chr6:43737936-43738472	K562	blood:	n/a	n/a
33	CHD2	chr6:43738322-43738459	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:43738182-43739941	A549	lung:	n/a	n/a
35	POLR2A	chr6:43737294-43740690	K562	blood:	n/a	n/a
36	POLR2A	chr6:43737317-43738681	K562	blood:	n/a	n/a
37	HA-E2F1	chr6:43738259-43740093	Hela-S3	cervix:	n/a	chr6:43739067-43739077 chr6:43739208-43739217 chr6:43739424-43739436 chr6:43739315-43739327
38	UBTF	chr6:43737726-43739963	K562	blood:	n/a	n/a
39	POLR2A	chr6:43738176-43738890	H1-hESC	embryonic stem cell:	n/a	n/a
40	IRF1	chr6:43737223-43738461	K562	blood:	n/a	n/a
41	YY1	chr6:43738180-43739069	K562	blood:	n/a	n/a
42	POLR2A	chr6:43737272-43738552	HepG2	liver:	n/a	n/a
43	POLR2A	chr6:43737070-43746379	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr6:43737082-43741495	H1-hESC	embryonic stem cell:	n/a	n/a
45	ZBTB7A	chr6:43738141-43741505	ECC-1	luminal epithelium:	n/a	chr6:43740506-43740515 chr6:43739932-43739939 chr6:43739207-43739216
46	ZBTB7A	chr6:43737001-43741490	ECC-1	luminal epithelium:	n/a	chr6:43740506-43740515 chr6:43737372-43737381 chr6:43739932-43739939 chr6:43739207-43739216
47	ELF1	chr6:43738119-43738913	K562	blood:	n/a	n/a
48	E2F6	chr6:43738235-43738962	K562	blood:	n/a	n/a
49	POLR2A	chr6:43737429-43739940	HEK293	kidney:	n/a	n/a
50	ZNF263	chr6:43738342-43739120	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:32174331..32175012-chr6:43738085..43738944,2	Hela-S3	cervix:
2	chr6:43738049..43742352-chr6:44213795..44216744,7	K562	blood:
3	chr20:60962198..60962719-chr6:43737546..43738450,2	NB4	blood:
4	chr6:43738039..43738759-chr8:145641815..145642530,2	Hela-S3	cervix:
5	chr6:43595036..43601855-chr6:43735920..43743852,18	K562	blood:
6	chr6:43592224..43600252-chr6:43737312..43744228,11	MCF-7	breast:
7	chr6:43737972..43738858-chr7:27779375..27780262,2	Hela-S3	cervix:
8	chr12:52446283..52447249-chr6:43738297..43739035,2	Hela-S3	cervix:
9	chr2:61404158..61404719-chr6:43737508..43738351,2	Hela-S3	cervix:
10	chr6:43737968..43738716-chr6:88411322..88411973,2	Hela-S3	cervix:
11	chr6:43655438..43657239-chr6:43736539..43739702,4	K562	blood:
12	chr6:43736441..43745894-chr6:44037513..44049664,39	K562	blood:
13	chr6:43736340..43742918-chr6:44039360..44044949,13	MCF-7	breast:
14	chr1:45186107..45187653-chr6:43737914..43739450,2	MCF-7	breast:
15	chr3:48481366..48482090-chr6:43738300..43738891,2	Hela-S3	cervix:
16	chr6:43737463..43739501-chr6:43819838..43821397,2	K562	blood:
17	chr6:43594866..43599640-chr6:43736940..43745540,22	K562	blood:
18	chr6:13614758..13615482-chr6:43737724..43738442,2	Hela-S3	cervix:
19	chr3:49066382..49067198-chr6:43737788..43738490,2	HCT-116	colon:
20	chr6:43594889..43598378-chr6:43738091..43741681,4	MCF-7	breast:
21	chr6:43730164..43744120-chr6:44034600..44052665,50	K562	blood:
22	chr6:43540602..43545091-chr6:43737636..43739851,4	MCF-7	breast:
23	chr6:43736197..43742093-chr6:44038080..44048969,27	MCF-7	breast:
24	chr6:43737638..43739422-chr7:75987482..75989449,2	MCF-7	breast:
25	chr12:120729544..120730197-chr6:43737793..43738450,2	Hela-S3	cervix:
26	chr4:79696772..79697553-chr6:43737917..43738589,2	Hela-S3	cervix:
27	chr6:43654019..43657239-chr6:43735769..43739176,4	K562	blood:
28	chr2:101618126..101619019-chr6:43737435..43738432,2	Hela-S3	cervix:
29	chr6:43601913..43603816-chr6:43737838..43740214,2	K562	blood:
30	chr6:43700705..43714068-chr6:43733889..43742277,18	K562	blood:
31	chr12:118454191..118455028-chr6:43737829..43738504,2	Hela-S3	cervix:
32	chr6:12008600..12009379-chr6:43737966..43738894,2	Hela-S3	cervix:
33	chr6:43737558..43739220-chr6:43817395..43820226,2	MCF-7	breast:
34	chr6:27859614..27862396-chr6:43737260..43739331,2	K562	blood:
35	chr6:43738064..43739006-chr8:80942016..80942619,2	Hela-S3	cervix:
36	chr11:62432613..62433305-chr6:43738242..43738785,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RSPH9-3	chr6:43737962-43738756	NONHSAT112918

Variant related genes	Relation type
VEGFA	TF binding region
ENSG00000071082	Chromatin interaction
ENSG00000173209	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000223469	Chromatin interaction
ENSG00000236961	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000096080	Chromatin interaction
ENSG00000124571	Chromatin interaction
ENSG00000135334	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000223947	Chromatin interaction
ENSG00000172432	Chromatin interaction
ENSG00000272086	Chromatin interaction
ENSG00000164051	Chromatin interaction
ENSG00000111445	Chromatin interaction
ENSG00000147586	Chromatin interaction
ENSG00000170027	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000095951	Chromatin interaction
ENSG00000138756	Chromatin interaction
ENSG00000124688	Chromatin interaction
ENSG00000147804	Chromatin interaction
ENSG00000261071	Chromatin interaction
ENSG00000106052	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000171858	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000113384	Chromatin interaction
ENSG00000231881	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000170734	Chromatin interaction
ENSG00000237686	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000260278	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000229893	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs3024997	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3024998	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3025000	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs699946	0.96[ASN][1000 genomes]
rs735286	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs833060	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs833068	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs833069	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs865577	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869383	chr6:43505094-43752189	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
3	nsv1018626	chr6:43694649-43803732	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv885848	chr6:43732669-43753051	Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv3331607	chr6:43734924-43742622	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
6	nsv823682	chr6:43737985-43739013	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 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	chr6:43737200-43738600	Active TSS	Brain Germinal Matrix	brain
2	chr6:43737200-43739800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr6:43737200-43739800	Active TSS	Brain Angular Gyrus	brain
4	chr6:43737200-43740000	Active TSS	Rectal Smooth Muscle	rectum
5	chr6:43737200-43740400	Active TSS	Placenta Amnion	Placenta Amnion
6	chr6:43737200-43741000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr6:43737200-43741400	Active TSS	Brain Anterior Caudate	brain
8	chr6:43737200-43742000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:43737400-43738400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr6:43737400-43738400	Flanking Active TSS	Placenta	Placenta
11	chr6:43737400-43738400	Flanking Active TSS	HUVEC	blood vessel
12	chr6:43737400-43738600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:43737400-43738600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:43737400-43738800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
15	chr6:43737400-43738800	Active TSS	Brain Hippocampus Middle	brain
16	chr6:43737400-43738800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
17	chr6:43737400-43739000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:43737400-43739000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:43737400-43739600	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr6:43737400-43739600	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr6:43737400-43739800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:43737400-43739800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:43737400-43739800	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr6:43737400-43739800	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr6:43737400-43739800	Active TSS	Colon Smooth Muscle	Colon
26	chr6:43737400-43739800	Active TSS	Fetal Brain Female	brain
27	chr6:43737400-43739800	Active TSS	Lung	lung
28	chr6:43737400-43739800	Active TSS	Spleen	Spleen
29	chr6:43737400-43740000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
30	chr6:43737400-43740000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:43737400-43740000	Active TSS	NHLF	lung
32	chr6:43737400-43740200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:43737400-43740200	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr6:43737400-43740200	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr6:43737400-43740200	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr6:43737400-43740200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:43737400-43740200	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr6:43737400-43740200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr6:43737400-43740200	Active TSS	Ovary	ovary
40	chr6:43737400-43740400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:43737400-43740400	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr6:43737400-43740400	Active TSS	Psoas Muscle	Psoas
43	chr6:43737400-43740400	Active TSS	A549	lung
44	chr6:43737400-43740600	Active TSS	H1 Cell Line	embryonic stem cell
45	chr6:43737400-43740600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:43737400-43740600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:43737400-43740600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:43737400-43740600	Active TSS	Esophagus	oesophagus
49	chr6:43737400-43740800	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr6:43737400-43740800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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