Variant report

Variant	rs7863385
Chromosome Location	chr9:21335404-21335405
allele	A/C
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	HCFC1	chr9:21334378-21335890	Hela-S3	cervix:	n/a	n/a
2	STAT5A	chr9:21334776-21335797	GM12878	blood:	n/a	chr9:21335481-21335493 chr9:21335471-21335483 chr9:21335166-21335178 chr9:21335084-21335093 chr9:21335375-21335399 chr9:21335370-21335390 chr9:21335477-21335489 chr9:21335083-21335092
3	MAX	chr9:21334855-21335753	A549	lung:	n/a	chr9:21335505-21335515 chr9:21335469-21335479
4	POLR2A	chr9:21335170-21335449	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr9:21335117-21335611	PANC-1	pancreas:	n/a	n/a
6	EBF1	chr9:21334787-21335800	GM12878	blood:	n/a	n/a
7	POLR2A	chr9:21334912-21335803	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr9:21335134-21335657	HUVEC	blood vessel:	n/a	n/a
9	BCLAF1	chr9:21334845-21335704	GM12878	blood:	n/a	chr9:21335213-21335226
10	POLR2A	chr9:21334642-21335776	GM12878	blood:	n/a	n/a
11	STAT3	chr9:21335220-21335420	MCF10A-Er-Src	breast:	n/a	chr9:21335370-21335390
12	MYC	chr9:21335031-21335467	MCF-7	breast:	n/a	n/a
13	STAT5A	chr9:21334956-21335501	GM12878	blood:	n/a	chr9:21335481-21335493 chr9:21335471-21335483 chr9:21335166-21335178 chr9:21335084-21335093 chr9:21335375-21335399 chr9:21335370-21335390 chr9:21335477-21335489 chr9:21335083-21335092
14	TCF7L2	chr9:21334694-21335407	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr9:21334981-21335762	SK-N-MC	brain:	n/a	n/a
16	POU2F2	chr9:21335007-21335667	GM12891	blood:	n/a	n/a
17	POLR2A	chr9:21335018-21335684	ECC-1	luminal epithelium:	n/a	n/a
18	YY1	chr9:21335145-21335509	A549	lung:	n/a	chr9:21335433-21335444 chr9:21335245-21335259 chr9:21335435-21335449
19	USF1	chr9:21335234-21335489	SK-N-SH_RA	brain:	n/a	n/a
20	MYC	chr9:21334458-21335796	NB4	blood:	n/a	chr9:21335505-21335515 chr9:21335469-21335479
21	RELA	chr9:21334611-21335720	GM18951	blood:	n/a	n/a
22	MAX	chr9:21334890-21335526	ECC-1	luminal epithelium:	n/a	chr9:21335505-21335515 chr9:21335469-21335479
23	POLR2A	chr9:21334938-21335707	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr9:21334763-21335739	Hela-S3	cervix:	n/a	n/a
25	GABPA	chr9:21334879-21335616	MCF-7	breast:	n/a	chr9:21335429-21335443 chr9:21335157-21335164
26	POLR2A	chr9:21334743-21335638	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr9:21334637-21335670	Hela-S3	cervix:	n/a	n/a
28	ZEB1	chr9:21334900-21335437	GM12878	blood:	n/a	n/a
29	TAF1	chr9:21335195-21335538	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr9:21334970-21335744	A549	lung:	n/a	n/a
31	POLR2A	chr9:21335071-21335491	H1-hESC	embryonic stem cell:	n/a	n/a
32	USF2	chr9:21335266-21335466	H1-hESC	embryonic stem cell:	n/a	n/a
33	HA-E2F1	chr9:21334766-21335404	MCF-7	breast:	n/a	n/a
34	REST	chr9:21335129-21335497	HepG2	liver:	n/a	chr9:21335197-21335210
35	POLR2A	chr9:21335134-21335492	PANC-1	pancreas:	n/a	n/a
36	SIN3A	chr9:21334660-21335687	H1-hESC	embryonic stem cell:	n/a	chr9:21335532-21335540 chr9:21335433-21335444
37	TAF1	chr9:21335078-21335552	HepG2	liver:	n/a	n/a
38	TAF1	chr9:21335154-21335458	GM12891	blood:	n/a	n/a
39	POLR2A	chr9:21335201-21335444	HepG2	liver:	n/a	n/a
40	ELF1	chr9:21334793-21335680	MCF-7	breast:	n/a	chr9:21335247-21335259
41	HEY1	chr9:21335119-21335709	HepG2	liver:	n/a	chr9:21335133-21335148
42	POLR2A	chr9:21334702-21335674	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr9:21334820-21335675	Hela-S3	cervix:	n/a	n/a
44	TCF12	chr9:21335015-21335472	GM12878	blood:	n/a	n/a
45	TAF1	chr9:21335137-21335549	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr9:21335065-21335655	A549	lung:	n/a	n/a
47	POLR2A	chr9:21334494-21335667	H1-hESC	embryonic stem cell:	n/a	n/a
48	EP300	chr9:21335151-21335608	SK-N-SH_RA	brain:	n/a	n/a
49	TAF1	chr9:21335019-21335656	SK-N-SH	brain:	n/a	n/a
50	SIN3AK20	chr9:21335206-21335439	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:174969137..174969741-chr9:21335404..21336059,2	NB4	blood:
2	chr12:10875091..10875955-chr9:21334907..21335831,2	NB4	blood:
3	chr9:21334810..21337205-chr9:21800546..21802816,2	MCF-7	breast:
4	chr5:138629198..138630197-chr9:21335314..21335966,2	NB4	blood:

Variant related genes	Relation type
KLHL9	TF binding region
ENSG00000264545	Chromatin interaction
ENSG00000015479	Chromatin interaction
ENSG00000099810	Chromatin interaction
ENSG00000060138	Chromatin interaction
ENSG00000120725	Chromatin interaction
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10114175	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10114825	1.00[CEU][hapmap]
rs11999696	0.94[EUR][1000 genomes]
rs12000461	0.94[EUR][1000 genomes]
rs12002231	0.87[EUR][1000 genomes]
rs12006448	1.00[CEU][hapmap]
rs12336789	0.97[EUR][1000 genomes]
rs12337907	1.00[CEU][hapmap]
rs12340718	0.97[EUR][1000 genomes]
rs17334047	0.97[EUR][1000 genomes]
rs2104880	1.00[MEX][hapmap]
rs28383780	0.94[EUR][1000 genomes]
rs35000944	0.94[EUR][1000 genomes]
rs35101870	0.97[EUR][1000 genomes]
rs35353365	0.97[EUR][1000 genomes]
rs3919593	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs41270127	1.00[EUR][1000 genomes]
rs41270129	1.00[EUR][1000 genomes]
rs41270131	1.00[EUR][1000 genomes]
rs41270133	1.00[EUR][1000 genomes]
rs41270135	1.00[EUR][1000 genomes]
rs6475532	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7037805	0.87[EUR][1000 genomes]
rs72691656	0.92[EUR][1000 genomes]
rs72691682	0.87[EUR][1000 genomes]
rs72691685	0.87[EUR][1000 genomes]
rs72691698	0.82[EUR][1000 genomes]
rs72691699	0.87[EUR][1000 genomes]
rs72691700	0.87[EUR][1000 genomes]
rs72691701	0.87[EUR][1000 genomes]
rs72691939	0.84[EUR][1000 genomes]
rs72691942	0.84[EUR][1000 genomes]
rs72691948	0.84[EUR][1000 genomes]
rs72693703	0.87[EUR][1000 genomes]
rs72693705	0.87[EUR][1000 genomes]
rs72695780	0.94[EUR][1000 genomes]
rs72695784	0.94[EUR][1000 genomes]
rs72695785	0.94[EUR][1000 genomes]
rs72695788	0.94[EUR][1000 genomes]
rs72695795	0.94[EUR][1000 genomes]
rs72695797	0.94[EUR][1000 genomes]
rs72695798	0.94[EUR][1000 genomes]
rs72695801	1.00[EUR][1000 genomes]
rs72697305	1.00[EUR][1000 genomes]
rs72697307	1.00[EUR][1000 genomes]
rs72697311	1.00[EUR][1000 genomes]
rs72697312	1.00[EUR][1000 genomes]
rs72697313	1.00[EUR][1000 genomes]
rs72697314	1.00[EUR][1000 genomes]
rs72697315	1.00[EUR][1000 genomes]
rs72697317	1.00[EUR][1000 genomes]
rs72697321	0.97[EUR][1000 genomes]
rs72697322	0.97[EUR][1000 genomes]
rs72697324	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72697326	0.97[EUR][1000 genomes]
rs72697327	0.97[EUR][1000 genomes]
rs72699197	0.97[EUR][1000 genomes]
rs72699198	0.97[EUR][1000 genomes]
rs72699199	0.97[EUR][1000 genomes]
rs72699200	0.97[EUR][1000 genomes]
rs72699201	0.97[EUR][1000 genomes]
rs72699202	0.97[EUR][1000 genomes]
rs72701303	0.97[EUR][1000 genomes]
rs72701305	0.97[EUR][1000 genomes]
rs72701306	0.97[EUR][1000 genomes]
rs72701307	0.97[EUR][1000 genomes]
rs72701308	0.97[EUR][1000 genomes]
rs72701309	0.97[EUR][1000 genomes]
rs72701311	0.97[EUR][1000 genomes]
rs72701312	0.97[EUR][1000 genomes]
rs72701313	0.97[EUR][1000 genomes]
rs72701314	0.97[EUR][1000 genomes]
rs72701315	0.97[EUR][1000 genomes]
rs72701316	0.97[EUR][1000 genomes]
rs72701317	0.97[EUR][1000 genomes]
rs72701318	0.97[EUR][1000 genomes]
rs72701319	0.97[EUR][1000 genomes]
rs72701320	0.97[EUR][1000 genomes]
rs72701321	0.94[EUR][1000 genomes]
rs7849714	0.85[AFR][1000 genomes]
rs7862030	1.00[CEU][hapmap];0.84[TSI][hapmap];0.97[EUR][1000 genomes]
rs7865334	0.94[EUR][1000 genomes]
rs9333355	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs9333356	1.00[CEU][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
2	nsv892736	chr9:21327141-21391698	Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21333000-21336000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr9:21333600-21335800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:21333600-21335800	Active TSS	Colonic Mucosa	Colon
4	chr9:21333800-21335800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr9:21333800-21335800	Active TSS	Lung	lung
6	chr9:21333800-21335800	Active TSS	NHLF	lung
7	chr9:21334000-21335600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr9:21334000-21335800	Active TSS	H1 Cell Line	embryonic stem cell
9	chr9:21334000-21335800	Active TSS	H9 Cell Line	embryonic stem cell
10	chr9:21334000-21335800	Active TSS	Right Ventricle	heart
11	chr9:21334200-21335600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:21334200-21335600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:21334200-21335600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:21334200-21335600	Active TSS	HSMM	muscle
15	chr9:21334200-21335800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:21334200-21335800	Active TSS	Muscle Satellite Cultured Cells	--
17	chr9:21334200-21335800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:21334200-21335800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:21334200-21335800	Active TSS	Aorta	Aorta
20	chr9:21334200-21335800	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr9:21334200-21335800	Active TSS	Fetal Intestine Small	intestine
22	chr9:21334200-21335800	Active TSS	Fetal Muscle Trunk	muscle
23	chr9:21334200-21335800	Active TSS	Fetal Muscle Leg	muscle
24	chr9:21334200-21335800	Active TSS	Placenta	Placenta
25	chr9:21334200-21335800	Active TSS	Left Ventricle	heart
26	chr9:21334200-21335800	Active TSS	Ovary	ovary
27	chr9:21334200-21335800	Active TSS	Placenta Amnion	Placenta Amnion
28	chr9:21334200-21335800	Active TSS	Psoas Muscle	Psoas
29	chr9:21334200-21335800	Active TSS	Right Atrium	heart
30	chr9:21334200-21335800	Active TSS	A549	lung
31	chr9:21334200-21335800	Active TSS	HSMMtube	muscle
32	chr9:21334200-21336000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:21334200-21336000	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr9:21334200-21336000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr9:21334200-21336000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:21334200-21336000	Active TSS	Colon Smooth Muscle	Colon
37	chr9:21334200-21336000	Active TSS	Fetal Intestine Large	intestine
38	chr9:21334200-21336000	Active TSS	Fetal Kidney	kidney
39	chr9:21334200-21336000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr9:21334200-21336000	Active TSS	Fetal Lung	lung
41	chr9:21334200-21336000	Active TSS	Stomach Smooth Muscle	stomach
42	chr9:21334200-21336000	Active TSS	NHDF-Ad	bronchial
43	chr9:21334400-21335600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:21334400-21335600	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr9:21334400-21335600	Active TSS	Fetal Heart	heart
46	chr9:21334400-21335600	Active TSS	Dnd41	blood
47	chr9:21334400-21335600	Active TSS	NHEK	skin
48	chr9:21334400-21335800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr9:21334400-21335800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:21334400-21335800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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