Variant report

Variant	rs9468236
Chromosome Location	chr6:27806434-27806435
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:467)
CpG islands
(count:61)
Chromatin interactive
region (count:36)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:467 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF3	chr6:27806125-27806483	HepG2	liver:	n/a	chr6:27806228-27806239 chr6:27806224-27806241 chr6:27806228-27806242 chr6:27806229-27806242 chr6:27806228-27806241 chr6:27806227-27806241
2	GATA1	chr6:27804212-27806599	PBDE	blood:	n/a	chr6:27805618-27805625 chr6:27804482-27804499
3	MAX	chr6:27804629-27806836	GM12878	blood:	n/a	n/a
4	SIN3AK20	chr6:27805535-27806988	HepG2	liver:	n/a	n/a
5	TAF1	chr6:27805629-27806934	Hela-S3	cervix:	n/a	n/a
6	FOS	chr6:27806020-27806492	MCF10A-Er-Src	breast:	n/a	chr6:27806307-27806315 chr6:27806241-27806250
7	CBX3	chr6:27805567-27806798	K562	blood:	n/a	n/a
8	GATA2	chr6:27806175-27806858	K562	blood:	n/a	n/a
9	JUN	chr6:27805967-27806518	K562	blood:	n/a	chr6:27806307-27806315 chr6:27806241-27806250
10	TCF12	chr6:27805858-27806851	HepG2	liver:	n/a	n/a
11	SP1	chr6:27805729-27806952	HepG2	liver:	n/a	chr6:27806265-27806286 chr6:27806238-27806259
12	POLR2A	chr6:27804476-27806957	K562	blood:	n/a	n/a
13	CHD2	chr6:27804592-27806567	Hela-S3	cervix:	n/a	chr6:27805473-27805483
14	POLR2A	chr6:27804355-27807788	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:27804437-27807892	Hela-S3	cervix:	n/a	n/a
16	TAF7	chr6:27804584-27806578	H1-hESC	embryonic stem cell:	n/a	n/a
17	CBX3	chr6:27804462-27806649	K562	blood:	n/a	n/a
18	NFYB	chr6:27806025-27806444	GM12878	blood:	n/a	chr6:27806273-27806287 chr6:27806210-27806225 chr6:27806239-27806249 chr6:27806236-27806248 chr6:27806237-27806252 chr6:27806234-27806249
19	CHD1	chr6:27804111-27807828	GM12878	blood:	n/a	chr6:27805473-27805483
20	POLR2A	chr6:27804384-27808058	MCF-7	breast:	n/a	n/a
21	BCLAF1	chr6:27802551-27808286	K562	blood:	n/a	chr6:27803234-27803242
22	ELK4	chr6:27806035-27806612	Hela-S3	cervix:	n/a	n/a
23	STAT5A	chr6:27804634-27806516	GM12878	blood:	n/a	chr6:27806465-27806489
24	POLR2A	chr6:27804577-27807240	GM12892	blood:	n/a	n/a
25	RUNX3	chr6:27804643-27806592	GM12878	blood:	n/a	chr6:27806250-27806259 chr6:27806250-27806259
26	BCLAF1	chr6:27805902-27806569	GM12878	blood:	n/a	n/a
27	ZC3H11A	chr6:27805948-27806572	K562	blood:	n/a	n/a
28	REST	chr6:27805635-27806903	SK-N-SH	brain:	n/a	n/a
29	EP300	chr6:27805999-27806516	GM12878	blood:	n/a	chr6:27806225-27806239
30	PBX3	chr6:27805896-27806581	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr6:27805153-27806936	GM12878	blood:	n/a	n/a
32	CREB1	chr6:27805904-27806455	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr6:27804370-27807327	GM12878	blood:	n/a	n/a
34	ZNF143	chr6:27805945-27806445	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:27804313-27807755	HCT-116	colon:	n/a	n/a
36	PML	chr6:27805860-27806490	GM12878	blood:	n/a	n/a
37	MYC	chr6:27804641-27806844	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr6:27806300-27806450	HCFaa	heart:	n/a	n/a
39	CHD2	chr6:27804593-27806485	GM12878	blood:	n/a	chr6:27805473-27805483
40	GTF2F1	chr6:27804566-27806925	Hela-S3	cervix:	n/a	n/a
41	HA-E2F1	chr6:27805341-27806481	MCF-7	breast:	n/a	chr6:27806076-27806087 chr6:27806087-27806098
42	POU2F2	chr6:27806252-27806545	GM12878	blood:	n/a	n/a
43	YY1	chr6:27806356-27806684	A549	lung:	n/a	n/a
44	REST	chr6:27806240-27806478	SK-N-SH	brain:	n/a	n/a
45	ZMIZ1	chr6:27804289-27806580	K562	blood:	n/a	n/a
46	POLR2A	chr6:27803974-27807891	H1-hESC	embryonic stem cell:	n/a	n/a
47	TAF1	chr6:27805724-27806771	Hela-S3	cervix:	n/a	n/a
48	MYC	chr6:27805975-27806493	MCF10A-Er-Src	breast:	n/a	n/a
49	STAT3	chr6:27806153-27806483	MCF10A-Er-Src	breast:	n/a	n/a
50	SIN3AK20	chr6:27805606-27806884	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:27806393-27806443	AG04449	skin:	fetal
2	chr6:27806393-27806443	PrEC	prostate:	n/a
3	chr6:27806393-27806443	NT2-D1	testis:	n/a
4	chr6:27806393-27806443	BJ	skin:	n/a
5	chr6:27806393-27806443	CMK	blood:	n/a
6	chr6:27806393-27806443	SK-N-SH	brain:	n/a
7	chr6:27806393-27806443	HRCEpiC	kidney:	n/a
8	chr6:27806393-27806443	HRPEpiC	eye:	n/a
9	chr6:27806393-27806443	HCF	heart:	n/a
10	chr6:27806393-27806443	Hepatocyte	liver:	n/a
11	chr6:27806393-27806443	HEK293	kidney:	embryo
12	chr6:27806393-27806443	HepG2	liver:	n/a
13	chr6:27806393-27806443	HCT-116	colon:	n/a
14	chr6:27806393-27806443	U87	brain:	n/a
15	chr6:27806393-27806443	ECC-1	luminal epithelium:	n/a
16	chr6:27806393-27806443	PANC-1	pancreas:	n/a
17	chr6:27806393-27806443	ProgFib	skin:	n/a
18	chr6:27806393-27806443	HIPEpiC	eye:	n/a
19	chr6:27806393-27806443	NH-A	brain:	n/a
20	chr6:27806393-27806443	HCPEpiC	choroid plexus:	n/a
21	chr6:27806393-27806443	HCM	heart:	n/a
22	chr6:27806393-27806443	K562	blood:	n/a
23	chr6:27806393-27806443	SKMC	muscle:	n/a
24	chr6:27806393-27806443	SK-N-MC	brain:	n/a
25	chr6:27806393-27806443	Hela-S3	cervix:	n/a
26	chr6:27806393-27806443	GM12878	blood:	n/a
27	chr6:27806393-27806443	H1-hESC	embryonic stem cell:	embryo
28	chr6:27806393-27806443	GM19239	blood:	n/a
29	chr6:27806393-27806443	NB4	blood:	n/a
30	chr6:27806393-27806443	HRE	kidney:	n/a
31	chr6:27806393-27806443	AG10803	skin:	n/a
32	chr6:27806393-27806443	AG04450	lung:	fetal
33	chr6:27806393-27806443	HAEpiC	amniotic membrane:	n/a
34	chr6:27806393-27806443	AG09319	gingival:	n/a
35	chr6:27806393-27806443	HUVEC	blood vessel:	n/a
36	chr6:27806393-27806443	HMEC	breast:	n/a
37	chr6:27806393-27806443	HPAEpiC	pulmonary alveolar:	n/a
38	chr6:27806393-27806443	HEEpiC	esophagus:	n/a
39	chr6:27806393-27806443	MCF10A-Er-Src	breast:	n/a
40	chr6:27806393-27806443	PFSK-1	brain:	n/a
41	chr6:27806393-27806443	HNPCEpiC	eye:	n/a
42	chr6:27806393-27806443	A549	lung:	n/a
43	chr6:27806393-27806443	RPTEC	kidney:	n/a
44	chr6:27806393-27806443	SAEC	small airway:	n/a
45	chr6:27806393-27806443	Caco-2	colon:	n/a
46	chr6:27806393-27806443	NHBE	bronchial:	n/a
47	chr6:27806393-27806443	Jurkat	blood:	n/a
48	chr6:27806393-27806443	IMR90	lung:	fetal
49	chr6:27806393-27806443	GM12892	blood:	n/a
50	chr6:27806393-27806443	BE2_C	brain:	n/a

(count:36 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26214556..26218152-chr6:27805510..27808232,3	K562	blood:
2	chr6:26124217..26124895-chr6:27806411..27807255,2	Hela-S3	cervix:
3	chr17:56756481..56757093-chr6:27805992..27806962,2	Hela-S3	cervix:
4	chr6:27805926..27806625-chr9:130212885..130213753,2	Hela-S3	cervix:
5	chr6:27805809..27807448-chr6:28184413..28187037,2	MCF-7	breast:
6	chr6:26216271..26217870-chr6:27804676..27807375,2	MCF-7	breast:
7	chr3:9438278..9439210-chr6:27806144..27806665,2	Hela-S3	cervix:
8	chr1:119682955..119683529-chr6:27806277..27807071,2	Hela-S3	cervix:
9	chr6:27098188..27105257-chr6:27800590..27808222,20	K562	blood:
10	chr6:26026035..26027624-chr6:27806330..27807928,2	K562	blood:
11	chr1:27189419..27190137-chr6:27805713..27806439,2	Hela-S3	cervix:
12	chr6:27100704..27101261-chr6:27805947..27806615,2	HCT-116	colon:
13	chr6:26102660..26104205-chr6:27804912..27807560,2	MCF-7	breast:
14	chr6:27805383..27807774-chr6:28104061..28105899,2	MCF-7	breast:
15	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
16	chr6:26024775..26027574-chr6:27806170..27808884,2	MCF-7	breast:
17	chr6:26029609..26032521-chr6:27805360..27808240,3	MCF-7	breast:
18	chr6:27805063..27806692-chrX:69644686..69647286,2	MCF-7	breast:
19	chr6:27804731..27806517-chr6:28302178..28303810,2	MCF-7	breast:
20	chr10:94449237..94450232-chr6:27805942..27806496,2	NB4	blood:
21	chr1:173792439..173793277-chr6:27806309..27807278,2	Hela-S3	cervix:
22	chr6:27805460..27807795-chr6:28047138..28049507,2	MCF-7	breast:
23	chr6:26020896..26022698-chr6:27805218..27807913,2	MCF-7	breast:
24	chr6:26156285..26158369-chr6:27805497..27807966,2	K562	blood:
25	chr3:49131901..49134800-chr6:27804680..27807035,2	K562	blood:
26	chr6:27805731..27807802-chr6:27860576..27861707,5	Hela-S3	cervix:
27	chr6:27805923..27806605-chr6:27860576..27861108,2	NB4	blood:
28	chr6:27806319..27806852-chr8:103667961..103668475,2	HCT-116	colon:
29	chr6:27803974..27806831-chr6:28047434..28050953,3	K562	blood:
30	chr6:27111071..27119431-chr6:27801399..27810552,22	K562	blood:
31	chr6:26154851..26161490-chr6:27803982..27809302,10	MCF-7	breast:
32	chr6:26248548..26251573-chr6:27804548..27807242,3	MCF-7	breast:
33	chr6:26251588..26253194-chr6:27805528..27807609,2	MCF-7	breast:
34	chr6:27113200..27117534-chr6:27802228..27806893,11	MCF-7	breast:
35	chr6:26054979..26056713-chr6:27806110..27807728,2	MCF-7	breast:
36	chr6:26204681..26207115-chr6:27805289..27807793,3	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H2AK	TF binding region
HIST1H2BN	TF binding region
HIST1H2BN	CpG island
HIST1H2AK	CpG island
ENSG00000256316	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000152804	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000231365	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000272009	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000130055	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000155090	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000175793	Chromatin interaction
ENSG00000116874	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000197958	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000197061	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12181629	0.90[ASN][1000 genomes]
rs2021835	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269277	1.00[ASN][1000 genomes]
rs9461403	0.85[TSI][hapmap]
rs9461412	1.00[ASW][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs9461418	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9468226	1.00[TSI][hapmap]
rs9468230	1.00[YRI][hapmap]
rs9468242	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468243	1.00[JPT][hapmap];1.00[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	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	nsv969367	chr6:27805874-27807512	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	64 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27802800-27808200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:27803200-27807400	Active TSS	K562	blood
3	chr6:27803200-27807600	Active TSS	Fetal Thymus	thymus
4	chr6:27803200-27808200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:27803400-27808000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:27803400-27808400	Active TSS	GM12878-XiMat	blood
7	chr6:27803800-27807800	Active TSS	Fetal Intestine Large	intestine
8	chr6:27803800-27808200	Active TSS	Thymus	Thymus
9	chr6:27804000-27807600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:27804000-27807800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:27804000-27808000	Active TSS	H1 Cell Line	embryonic stem cell
12	chr6:27804000-27808000	Active TSS	HSMMtube	muscle
13	chr6:27804000-27808200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:27804200-27806800	Active TSS	Fetal Muscle Trunk	muscle
15	chr6:27804200-27807200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:27804200-27807400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:27804200-27807400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
18	chr6:27804200-27807600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:27804200-27807600	Active TSS	Aorta	Aorta
20	chr6:27804200-27807800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr6:27804200-27807800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
22	chr6:27804200-27807800	Active TSS	Psoas Muscle	Psoas
23	chr6:27804200-27808000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:27804200-27808000	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr6:27804200-27808000	Active TSS	A549	lung
26	chr6:27804400-27806800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:27804400-27806800	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr6:27804400-27806800	Active TSS	Fetal Stomach	stomach
29	chr6:27804400-27807000	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr6:27804400-27807400	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr6:27804400-27807400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:27804400-27807400	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr6:27804400-27807400	Active TSS	Colon Smooth Muscle	Colon
34	chr6:27804400-27807600	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr6:27804400-27807600	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr6:27804400-27807600	Active TSS	Colonic Mucosa	Colon
37	chr6:27804400-27807600	Active TSS	Fetal Intestine Small	intestine
38	chr6:27804400-27807600	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr6:27804400-27807800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr6:27804400-27807800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:27804400-27807800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:27804400-27807800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:27804400-27807800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:27804400-27807800	Active TSS	Fetal Heart	heart
45	chr6:27804400-27807800	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr6:27804400-27807800	Active TSS	NHDF-Ad	bronchial
47	chr6:27804400-27807800	Active TSS	NHLF	lung
48	chr6:27804400-27808000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:27804400-27808000	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr6:27804400-27808000	Active TSS	Hela-S3	cervix

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