Variant report

Variant	rs9639027
Chromosome Location	chr7:6746738-6746739
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	HEY1	chr7:6746109-6747028	HepG2	liver:	n/a	chr7:6746585-6746600 chr7:6746276-6746291 chr7:6746315-6746330 chr7:6746442-6746457 chr7:6746189-6746204
2	BRCA1	chr7:6746551-6747053	Hela-S3	cervix:	n/a	n/a
3	MAX	chr7:6745522-6747213	A549	lung:	n/a	chr7:6745893-6745902 chr7:6746006-6746013 chr7:6746619-6746629
4	ELF1	chr7:6746334-6746822	HepG2	liver:	n/a	chr7:6746336-6746345 chr7:6746636-6746649 chr7:6746577-6746589
5	POLR2A	chr7:6746360-6746964	K562	blood:	n/a	n/a
6	POLR2A	chr7:6746250-6747054	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr7:6746236-6746996	K562	blood:	n/a	n/a
8	GABPA	chr7:6745888-6747239	SK-N-SH	brain:	n/a	chr7:6746589-6746600 chr7:6746623-6746632 chr7:6746621-6746635 chr7:6746591-6746600 chr7:6746589-6746598 chr7:6746443-6746452 chr7:6746586-6746600 chr7:6746445-6746454 chr7:6746589-6746603 chr7:6746621-6746632
9	ZBTB33	chr7:6746430-6746811	HepG2	liver:	n/a	n/a
10	TCF12	chr7:6746158-6747024	A549	lung:	n/a	n/a
11	MAFK	chr7:6746538-6747041	K562	blood:	n/a	n/a
12	CUX1	chr7:6746604-6746983	K562	blood:	n/a	n/a
13	HEY1	chr7:6746292-6746942	K562	blood:	n/a	chr7:6746585-6746600 chr7:6746315-6746330 chr7:6746442-6746457
14	POLR2A	chr7:6745936-6746938	GM15510	blood:	n/a	n/a
15	YY1	chr7:6746617-6746872	HCT-116	colon:	n/a	n/a
16	SMARCB1	chr7:6745707-6746778	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr7:6746338-6746809	HEK293	kidney:	n/a	n/a
18	ELK4	chr7:6746481-6746919	HEK293	kidney:	n/a	chr7:6746640-6746649 chr7:6746640-6746648 chr7:6746639-6746650
19	TAF1	chr7:6746341-6746928	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr7:6746213-6746964	GM12892	blood:	n/a	n/a
21	POLR2A	chr7:6746180-6747106	U87	brain:	n/a	n/a
22	E2F6	chr7:6746458-6746781	K562	blood:	n/a	chr7:6746622-6746631 chr7:6746590-6746599 chr7:6746662-6746672 chr7:6746469-6746484
23	MAX	chr7:6746223-6747031	ECC-1	luminal epithelium:	n/a	chr7:6746619-6746629
24	MAX	chr7:6746405-6746971	K562	blood:	n/a	chr7:6746619-6746629
25	YY1	chr7:6746350-6747023	GM12892	blood:	n/a	chr7:6746579-6746590 chr7:6746581-6746590 chr7:6746375-6746389
26	ATF3	chr7:6746344-6746860	A549	lung:	n/a	chr7:6746443-6746452
27	POLR2A	chr7:6746186-6747074	U87	brain:	n/a	n/a
28	POLR2A	chr7:6745751-6746850	A549	lung:	n/a	n/a
29	REST	chr7:6746355-6746903	A549	lung:	n/a	chr7:6746433-6746446
30	CHD2	chr7:6745687-6746766	K562	blood:	n/a	n/a
31	CBX3	chr7:6746385-6747206	K562	blood:	n/a	n/a
32	TAF1	chr7:6746176-6746787	K562	blood:	n/a	n/a
33	MAZ	chr7:6745629-6746859	K562	blood:	n/a	chr7:6745893-6745902 chr7:6746006-6746013
34	FOXA1	chr7:6746393-6746881	T-47D	breast:	n/a	n/a
35	STAT1	chr7:6746409-6747041	GM12878	blood:	n/a	chr7:6746424-6746436
36	POLR2A	chr7:6746299-6746939	K562	blood:	n/a	n/a
37	POLR2A	chr7:6745565-6746896	GM12892	blood:	n/a	n/a
38	GTF2F1	chr7:6746475-6747042	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr7:6746340-6746893	SK-N-SH	brain:	n/a	n/a
40	BHLHE40	chr7:6746435-6747008	K562	blood:	n/a	n/a
41	HCFC1	chr7:6746338-6746999	K562	blood:	n/a	n/a
42	POLR2A	chr7:6746033-6746947	ECC-1	luminal epithelium:	n/a	n/a
43	GABPA	chr7:6746395-6746954	K562	blood:	n/a	chr7:6746589-6746600 chr7:6746623-6746632 chr7:6746621-6746635 chr7:6746591-6746600 chr7:6746589-6746598 chr7:6746443-6746452 chr7:6746586-6746600 chr7:6746445-6746454 chr7:6746589-6746603 chr7:6746621-6746632
44	POLR2A	chr7:6746289-6747030	H1-neurons	neurons:	n/a	n/a
45	RFX5	chr7:6746433-6747005	Hela-S3	cervix:	n/a	n/a
46	CHD2	chr7:6746096-6747076	Hela-S3	cervix:	n/a	n/a
47	NRF1	chr7:6746410-6746817	Hela-S3	cervix:	n/a	chr7:6746589-6746600 chr7:6746623-6746632 chr7:6746621-6746635 chr7:6746591-6746600 chr7:6746620-6746631 chr7:6746589-6746598 chr7:6746443-6746452 chr7:6746588-6746599 chr7:6746586-6746600 chr7:6746445-6746454 chr7:6746589-6746603 chr7:6746621-6746632
48	YY1	chr7:6746388-6746830	A549	lung:	n/a	chr7:6746579-6746590 chr7:6746581-6746590
49	ZNF143	chr7:6746322-6747083	GM12878	blood:	n/a	chr7:6746646-6746664 chr7:6746444-6746454 chr7:6746696-6746715
50	MXI1	chr7:6746477-6746948	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:6746715-6746765	RPTEC	kidney:	n/a
2	chr7:6746688-6746738	GM12891	blood:	n/a
3	chr7:6746715-6746765	Caco-2	colon:	n/a
4	chr7:6746715-6746765	HL-60	blood:	n/a
5	chr7:6746715-6746765	GM06990	blood:	n/a
6	chr7:6746715-6746765	PrEC	prostate:	n/a
7	chr7:6746715-6746765	NT2-D1	testis:	n/a
8	chr7:6746715-6746765	SKMC	muscle:	n/a
9	chr7:6746715-6746765	H1-hESC	embryonic stem cell:	embryo
10	chr7:6746715-6746765	K562	blood:	n/a
11	chr7:6746715-6746765	Hela-S3	cervix:	n/a
12	chr7:6746688-6746738	AG04449	skin:	fetal
13	chr7:6746688-6746738	HL-60	blood:	n/a
14	chr7:6746715-6746765	SK-N-MC	brain:	n/a
15	chr7:6746688-6746738	MCF10A-Er-Src	breast:	n/a
16	chr7:6746688-6746738	NT2-D1	testis:	n/a
17	chr7:6746688-6746738	SK-N-SH_RA	brain:	n/a
18	chr7:6746688-6746738	AG10803	skin:	n/a
19	chr7:6746688-6746738	PANC-1	pancreas:	n/a
20	chr7:6746715-6746765	ovcar-3	ovarian:	n/a
21	chr7:6746715-6746765	HCM	heart:	n/a
22	chr7:6746688-6746738	HepG2	liver:	n/a
23	chr7:6746715-6746765	HRCEpiC	kidney:	n/a
24	chr7:6746688-6746738	HAEpiC	amniotic membrane:	n/a
25	chr7:6746715-6746765	HepG2	liver:	n/a
26	chr7:6746715-6746765	AG04449	skin:	fetal
27	chr7:6746688-6746738	HCT-116	colon:	n/a
28	chr7:6746688-6746738	K562	blood:	n/a
29	chr7:6746688-6746738	Hepatocyte	liver:	n/a
30	chr7:6746688-6746738	HEK293	kidney:	embryo
31	chr7:6746715-6746765	GM19239	blood:	n/a
32	chr7:6746715-6746765	HEK293	kidney:	embryo
33	chr7:6746688-6746738	HUVEC	blood vessel:	n/a
34	chr7:6746715-6746765	PFSK-1	brain:	n/a
35	chr7:6746688-6746738	SK-N-SH	brain:	n/a
36	chr7:6746688-6746738	GM06990	blood:	n/a
37	chr7:6746688-6746738	NHBE	bronchial:	n/a
38	chr7:6746715-6746765	NHDF-neo	bronchial:	n/a
39	chr7:6746715-6746765	AG10803	skin:	n/a
40	chr7:6746715-6746765	BJ	skin:	n/a
41	chr7:6746688-6746738	HRCEpiC	kidney:	n/a
42	chr7:6746715-6746765	BE2_C	brain:	n/a
43	chr7:6746715-6746765	CMK	blood:	n/a
44	chr7:6746688-6746738	PrEC	prostate:	n/a
45	chr7:6746715-6746765	HRPEpiC	eye:	n/a
46	chr7:6746688-6746738	GM19239	blood:	n/a
47	chr7:6746715-6746765	SK-N-SH_RA	brain:	n/a
48	chr7:6746715-6746765	HIPEpiC	eye:	n/a
49	chr7:6746715-6746765	HCF	heart:	n/a
50	chr7:6746688-6746738	MCF-7	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6745224..6747442-chr7:6767898..6770902,3	MCF-7	breast:
2	chr7:6746161..6747688-chr7:6768318..6771249,2	MCF-7	breast:
3	chr7:6681243..6682856-chr7:6746246..6748831,2	K562	blood:
4	chr7:6675962..6678642-chr7:6744432..6748032,4	MCF-7	breast:
5	chr7:6744871..6747873-chr7:6767656..6771321,4	K562	blood:
6	chr2:179315296..179317868-chr7:6745682..6748008,2	MCF-7	breast:
7	chr17:59484738..59486572-chr7:6745021..6746847,2	MCF-7	breast:
8	chr7:6676193..6679067-chr7:6744810..6746794,4	K562	blood:
9	chr7:6745463..6748475-chr7:6767656..6769994,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC073343.1-1	chr7:6746704-6748672	NONHSAT119061

Variant related genes	Relation type
ZNF12	TF binding region
PMS2CL	TF binding region
ZNF12	CpG island
PMS2CL	CpG island
ENSG00000180228	Chromatin interaction
ENSG00000187953	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000205903	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10244591	0.92[JPT][hapmap]
rs10272921	0.92[JPT][hapmap]
rs10441131	0.83[AMR][1000 genomes]
rs10951992	0.80[AFR][1000 genomes]
rs10951994	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs11979878	0.84[ASN][1000 genomes]
rs12531541	0.83[ASN][1000 genomes]
rs12535850	0.82[ASN][1000 genomes]
rs12537448	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs12673800	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs13224907	0.92[JPT][hapmap]
rs13247186	0.90[JPT][hapmap]
rs2140909	0.88[CHB][hapmap]
rs2881352	0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs3757481	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3757482	0.90[ASN][1000 genomes]
rs3757483	0.90[ASN][1000 genomes]
rs3801033	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs3801038	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801039	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs60514449	0.86[ASN][1000 genomes]
rs62439702	0.86[ASN][1000 genomes]
rs6463576	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6463578	0.88[ASN][1000 genomes]
rs6463579	0.86[AMR][1000 genomes]
rs6463580	0.92[JPT][hapmap];0.86[AMR][1000 genomes]
rs6944332	0.92[CHD][hapmap];0.92[JPT][hapmap]
rs6953825	0.92[JPT][hapmap]
rs6954172	0.92[CHD][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes]
rs6964079	0.81[CHD][hapmap]
rs6964276	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6966713	0.81[AMR][1000 genomes]
rs6967414	0.90[ASN][1000 genomes]
rs6969066	0.90[ASN][1000 genomes]
rs6971621	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs6972017	0.84[ASN][1000 genomes]
rs6974325	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs6979127	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs7779296	0.92[CHD][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs7782227	0.90[ASN][1000 genomes]
rs7786706	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7798471	0.84[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7804259	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv887439	chr7:6736332-6791749	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1015646	chr7:6738483-6779270	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv887440	chr7:6743097-6820508	Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv8038	chr7:6744717-6748111	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv887441	chr7:6744957-6919214	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	esv32852	chr7:6745984-6746850	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9639027	CYTH3	cis	lymphoblastoid	seeQTL
rs9639027	SDK1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6744600-6747200	Active TSS	Right Ventricle	heart
2	chr7:6744800-6746800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr7:6744800-6747200	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr7:6745000-6746800	Active TSS	Stomach Mucosa	stomach
5	chr7:6745000-6746800	Active TSS	GM12878-XiMat	blood
6	chr7:6745000-6746800	Active TSS	HMEC	breast
7	chr7:6745000-6747000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr7:6745000-6747000	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr7:6745000-6747000	Active TSS	Fetal Intestine Large	intestine
10	chr7:6745000-6747000	Active TSS	Stomach Smooth Muscle	stomach
11	chr7:6745000-6747200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr7:6745000-6747200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:6745000-6747200	Active TSS	Colonic Mucosa	Colon
14	chr7:6745000-6747200	Active TSS	Fetal Kidney	kidney
15	chr7:6745000-6747200	Active TSS	Ovary	ovary
16	chr7:6745000-6747200	Active TSS	Right Atrium	heart
17	chr7:6745000-6747400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:6745000-6747600	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr7:6745200-6746800	Active TSS	Rectal Smooth Muscle	rectum
20	chr7:6745200-6746800	Active TSS	Hela-S3	cervix
21	chr7:6745200-6746800	Active TSS	HSMM	muscle
22	chr7:6745200-6746800	Active TSS	K562	blood
23	chr7:6745200-6747000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:6745200-6747000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:6745200-6747000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr7:6745200-6747000	Active TSS	A549	lung
27	chr7:6745200-6747200	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr7:6745200-6747200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:6745200-6747200	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr7:6745200-6747200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:6745200-6747200	Active TSS	Left Ventricle	heart
32	chr7:6745200-6747200	Active TSS	Psoas Muscle	Psoas
33	chr7:6745200-6747200	Active TSS	NHDF-Ad	bronchial
34	chr7:6745200-6747400	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr7:6745200-6747400	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr7:6745200-6747400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr7:6745400-6746800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:6745400-6746800	Active TSS	Fetal Intestine Small	intestine
39	chr7:6745400-6746800	Active TSS	Fetal Lung	lung
40	chr7:6745400-6746800	Active TSS	HSMMtube	muscle
41	chr7:6745400-6746800	Active TSS	NHEK	skin
42	chr7:6745400-6747000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr7:6745400-6747000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr7:6745400-6747000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr7:6745400-6747000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr7:6745400-6747000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:6745400-6747200	Active TSS	Fetal Muscle Trunk	muscle
48	chr7:6745400-6747200	Active TSS	NHLF	lung
49	chr7:6745400-6747600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:6745600-6746800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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