Variant report

Variant	rs7020056
Chromosome Location	chr9:101544627-101544628
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	POLR2A	chr9:101544170-101544719	HCT-116	colon:	n/a	n/a
2	RCOR1	chr9:101544246-101544646	Hela-S3	cervix:	n/a	n/a
3	NR3C1	chr9:101544080-101544632	A549	lung:	n/a	chr9:101544391-101544405
4	SMARCC1	chr9:101544006-101544870	Hela-S3	cervix:	n/a	chr9:101544412-101544421
5	MAZ	chr9:101544239-101544710	Hela-S3	cervix:	n/a	n/a
6	FOS	chr9:101544215-101544692	MCF10A-Er-Src	breast:	n/a	chr9:101544413-101544421 chr9:101544412-101544422
7	EP300	chr9:101544249-101544668	Hela-S3	cervix:	n/a	n/a
8	USF2	chr9:101544357-101544665	Hela-S3	cervix:	n/a	chr9:101544544-101544555
9	TEAD4	chr9:101544135-101544644	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr9:101544149-101544895	Hela-S3	cervix:	n/a	n/a
11	JUND	chr9:101544047-101544887	HCT-116	colon:	n/a	chr9:101544411-101544422 chr9:101544413-101544421 chr9:101544412-101544422
12	MAFK	chr9:101544262-101544702	Hela-S3	cervix:	n/a	n/a
13	JUND	chr9:101544201-101544919	Hela-S3	cervix:	n/a	chr9:101544411-101544422 chr9:101544413-101544421 chr9:101544412-101544422
14	STAT3	chr9:101544288-101544686	Hela-S3	cervix:	n/a	n/a
15	MYC	chr9:101544384-101544646	MCF10A-Er-Src	breast:	n/a	n/a
16	TFAP2C	chr9:101543891-101544824	Hela-S3	cervix:	n/a	n/a
17	FOSL1	chr9:101544132-101544819	HCT-116	colon:	n/a	chr9:101544413-101544421 chr9:101544412-101544422
18	SP1	chr9:101544041-101544868	HCT-116	colon:	n/a	n/a
19	SP1	chr9:101543965-101544934	HCT-116	colon:	n/a	n/a
20	RFX5	chr9:101544270-101544822	Hela-S3	cervix:	n/a	n/a
21	TCF7L2	chr9:101544025-101544800	Hela-S3	cervix:	n/a	chr9:101544383-101544392
22	MYC	chr9:101544358-101544903	MCF10A-Er-Src	breast:	n/a	n/a
23	TCF12	chr9:101544211-101544905	ECC-1	luminal epithelium:	n/a	n/a
24	BRCA1	chr9:101544276-101544761	Hela-S3	cervix:	n/a	n/a
25	TBP	chr9:101544355-101544702	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr9:101544285-101544749	Hela-S3	cervix:	n/a	n/a
27	MAX	chr9:101544324-101544751	Hela-S3	cervix:	n/a	n/a
28	TEAD4	chr9:101544223-101544644	K562	blood:	n/a	n/a
29	NR2F2	chr9:101543994-101544672	MCF-7	breast:	n/a	n/a
30	SMC3	chr9:101544272-101544872	Hela-S3	cervix:	n/a	n/a
31	SPI1	chr9:101544401-101544823	HL-60	blood:	n/a	n/a
32	POLR2A	chr9:101542339-101545223	K562	blood:	n/a	n/a
33	CEBPB	chr9:101544352-101544993	Hela-S3	cervix:	n/a	chr9:101544834-101544845
34	JUND	chr9:101544052-101544927	HCT-116	colon:	n/a	chr9:101544411-101544422 chr9:101544413-101544421 chr9:101544412-101544422
35	CTCF	chr9:101544520-101544670	HMEC	breast:	n/a	n/a
36	TEAD4	chr9:101544179-101544709	ECC-1	luminal epithelium:	n/a	n/a
37	CTCF	chr9:101544555-101544668	NHEK	skin:	n/a	n/a
38	CTCF	chr9:101544603-101544638	Hela-S3	cervix:	n/a	n/a
39	CHD2	chr9:101544288-101544677	Hela-S3	cervix:	n/a	n/a
40	FOS	chr9:101544272-101544739	MCF10A-Er-Src	breast:	n/a	chr9:101544413-101544421 chr9:101544412-101544422
41	FOSL1	chr9:101544101-101544862	HCT-116	colon:	n/a	chr9:101544413-101544421 chr9:101544412-101544422

No.	Distal block	Cell Line	Cell type
1	chr9:101536018..101539234-chr9:101540914..101545931,7	K562	blood:
2	chr9:101543983..101545849-chr9:101571655..101573219,2	MCF-7	breast:
3	chr9:101542485..101545133-chr9:101546438..101549115,3	MCF-7	breast:
4	chr9:101525116..101528119-chr9:101542195..101544666,3	K562	blood:

Variant related genes	Relation type
ANKS6	TF binding region
ENSG00000165138	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10121153	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1022796	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10739690	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10760475	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10760479	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10760494	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10819266	0.87[ASN][1000 genomes]
rs10819308	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10819320	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10987747	0.80[ASW][hapmap];0.81[TSI][hapmap]
rs10987749	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11791440	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12056975	0.87[EUR][1000 genomes]
rs1543506	0.84[TSI][hapmap]
rs1555519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3933477	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742737	0.93[ASN][1000 genomes]
rs4742738	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs4742741	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4742745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743282	0.89[ASN][1000 genomes]
rs6478839	0.91[ASN][1000 genomes]
rs6478845	0.90[ASN][1000 genomes]
rs7018907	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7027405	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7027771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038640	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7047722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7357783	0.92[ASN][1000 genomes]
rs7469116	0.95[ASN][1000 genomes]
rs7853904	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7861186	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7865233	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9886821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7020056	C9orf130	cis	cerebellum	SCAN
rs7020056	ZNF189	cis	cerebellum	SCAN
rs7020056	ANKS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101494400-101553000	Weak transcription	Fetal Heart	heart
2	chr9:101496600-101549400	Weak transcription	Small Intestine	intestine
3	chr9:101506800-101553400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:101508600-101557400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr9:101514400-101553400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:101518800-101557200	Weak transcription	Psoas Muscle	Psoas
7	chr9:101521200-101557600	Weak transcription	Fetal Brain Male	brain
8	chr9:101526400-101549400	Strong transcription	Stomach Smooth Muscle	stomach
9	chr9:101530200-101547600	Weak transcription	NHDF-Ad	bronchial
10	chr9:101530400-101557800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:101533800-101553200	Strong transcription	Fetal Stomach	stomach
12	chr9:101534000-101557600	Weak transcription	Right Atrium	heart
13	chr9:101534400-101545800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr9:101535600-101553400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr9:101535800-101552000	Weak transcription	Thymus	Thymus
16	chr9:101535800-101553400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:101535800-101557400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr9:101536000-101553200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr9:101536000-101557600	Weak transcription	Primary B cells from cord blood	blood
20	chr9:101536200-101553400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:101536600-101557600	Weak transcription	Brain Germinal Matrix	brain
22	chr9:101536800-101545600	Weak transcription	HSMMtube	muscle
23	chr9:101536800-101546200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:101536800-101551400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr9:101536800-101551600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr9:101537000-101545000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:101537000-101557400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:101537400-101547000	Genic enhancers	Fetal Intestine Small	intestine
29	chr9:101537600-101549800	Weak transcription	Colon Smooth Muscle	Colon
30	chr9:101538200-101545600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr9:101538200-101553000	Weak transcription	NH-A	brain
32	chr9:101538800-101552400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:101539000-101546600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:101539000-101553000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:101539800-101546000	Weak transcription	Left Ventricle	heart
36	chr9:101540400-101545000	Enhancers	Fetal Intestine Large	intestine
37	chr9:101540400-101546600	Strong transcription	Pancreas	Pancrea
38	chr9:101541600-101545000	Weak transcription	Fetal Kidney	kidney
39	chr9:101541600-101547800	Weak transcription	Gastric	stomach
40	chr9:101541600-101553000	Weak transcription	Brain Anterior Caudate	brain
41	chr9:101542000-101553200	Weak transcription	HUVEC	blood vessel
42	chr9:101542400-101546800	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr9:101542600-101546200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr9:101542600-101546200	Weak transcription	Lung	lung
45	chr9:101542600-101548000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr9:101542600-101548000	Weak transcription	Fetal Thymus	thymus
47	chr9:101542600-101553200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:101542800-101547200	Strong transcription	Primary T cells from cord blood	blood
49	chr9:101543200-101546600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:101543200-101547000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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