Variant report

Variant	rs12535669
Chromosome Location	chr7:66205550-66205551
allele	C/G/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	POLR2A	chr7:66205218-66206323	GM12878	blood:	n/a	n/a
2	TCF12	chr7:66205243-66206393	ECC-1	luminal epithelium:	n/a	n/a
3	GABPA	chr7:66205310-66205819	H1-hESC	embryonic stem cell:	n/a	chr7:66205666-66205675
4	SIN3AK20	chr7:66205302-66205797	PFSK-1	brain:	n/a	n/a
5	FOSL2	chr7:66205302-66206647	HepG2	liver:	n/a	chr7:66205832-66205841
6	POLR2A	chr7:66205222-66206566	A549	lung:	n/a	n/a
7	POLR2A	chr7:66204970-66206735	GM12892	blood:	n/a	n/a
8	ELF1	chr7:66205137-66206275	MCF-7	breast:	n/a	chr7:66205434-66205445 chr7:66205435-66205444 chr7:66205612-66205623 chr7:66205658-66205670 chr7:66205371-66205383 chr7:66205613-66205622 chr7:66206238-66206250
9	ETS1	chr7:66205212-66205893	K562	blood:	n/a	chr7:66205344-66205357 chr7:66205588-66205595 chr7:66205584-66205597 chr7:66205434-66205443 chr7:66205614-66205623 chr7:66205664-66205675 chr7:66205614-66205623 chr7:66205834-66205845 chr7:66205615-66205625
10	SREBP2	chr7:66205272-66206564	GM12878	blood:	n/a	n/a
11	CEBPD	chr7:66205332-66205891	K562	blood:	n/a	n/a
12	NFIC	chr7:66205251-66205742	GM12878	blood:	n/a	n/a
13	POU2F2	chr7:66205158-66205867	GM12878	blood:	n/a	chr7:66205660-66205672
14	POLR2A	chr7:66205221-66206433	GM12878	blood:	n/a	n/a
15	CREB1	chr7:66205303-66205840	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr7:66205400-66205550	AG09319	gingival:	n/a	n/a
17	POLR2A	chr7:66204697-66206885	U87	brain:	n/a	n/a
18	YY1	chr7:66205305-66205761	H1-hESC	embryonic stem cell:	n/a	chr7:66205369-66205380 chr7:66205487-66205498 chr7:66205663-66205677 chr7:66205704-66205718 chr7:66205666-66205675
19	NR2F2	chr7:66205125-66205804	K562	blood:	n/a	n/a
20	POLR2A	chr7:66205332-66206304	HEK293	kidney:	n/a	n/a
21	SPI1	chr7:66205127-66206014	GM12878	blood:	n/a	n/a
22	REST	chr7:66205017-66206597	H1-neurons	neurons:	n/a	chr7:66205704-66205717 chr7:66205697-66205707 chr7:66206234-66206244 chr7:66206322-66206336 chr7:66205704-66205717 chr7:66206361-66206374 chr7:66205437-66205455 chr7:66205923-66205936 chr7:66205701-66205714
23	TCF7L2	chr7:66205370-66206142	HCT-116	colon:	n/a	n/a
24	MAX	chr7:66205360-66205974	H1-hESC	embryonic stem cell:	n/a	n/a
25	YY1	chr7:66204915-66206250	GM12878	blood:	n/a	chr7:66206236-66206250 chr7:66205369-66205380 chr7:66205487-66205498 chr7:66205663-66205677 chr7:66205704-66205718 chr7:66205666-66205675 chr7:66205836-66205845 chr7:66205834-66205845
26	YY1	chr7:66204855-66205890	GM12878	blood:	n/a	chr7:66205369-66205380 chr7:66205487-66205498 chr7:66205663-66205677 chr7:66205704-66205718 chr7:66205666-66205675 chr7:66205836-66205845 chr7:66205834-66205845
27	TAF1	chr7:66205321-66205714	A549	lung:	n/a	n/a
28	MXI1	chr7:66205247-66206317	HepG2	liver:	n/a	n/a
29	POLR2A	chr7:66205122-66206482	HUVEC	blood vessel:	n/a	n/a
30	NR2F2	chr7:66204481-66206561	K562	blood:	n/a	n/a
31	EP300	chr7:66205203-66206320	ECC-1	luminal epithelium:	n/a	chr7:66206237-66206253 chr7:66205698-66205714 chr7:66206246-66206262 chr7:66205615-66205622 chr7:66206234-66206250
32	POLR2A	chr7:66205162-66206530	A549	lung:	n/a	n/a
33	TAF1	chr7:66205313-66205866	H1-neurons	neurons:	n/a	n/a
34	ZNF384	chr7:66205352-66205755	K562	blood:	n/a	n/a
35	PBX3	chr7:66205372-66205875	A549	lung:	n/a	n/a
36	TAF1	chr7:66205202-66205871	MCF-7	breast:	n/a	n/a
37	SPI1	chr7:66205449-66205670	GM12878	blood:	n/a	n/a
38	TAF1	chr7:66205159-66205941	K562	blood:	n/a	n/a
39	TBP	chr7:66205161-66205938	GM12878	blood:	n/a	n/a
40	RCOR1	chr7:66204964-66206433	K562	blood:	n/a	n/a
41	CTCF	chr7:66205400-66205550	HA-sp	spinal cord:	n/a	n/a
42	SMC3	chr7:66205268-66206426	Hela-S3	cervix:	n/a	n/a
43	YY1	chr7:66204941-66205790	A549	lung:	n/a	chr7:66205369-66205380 chr7:66205487-66205498 chr7:66205663-66205677 chr7:66205704-66205718 chr7:66205666-66205675
44	HCFC1	chr7:66205255-66206198	K562	blood:	n/a	n/a
45	PAX5	chr7:66205012-66206054	GM12878	blood:	n/a	chr7:66205587-66205596
46	TAF1	chr7:66205121-66205880	GM12891	blood:	n/a	n/a
47	TAF1	chr7:66205156-66206290	SK-N-SH	brain:	n/a	n/a
48	CREB1	chr7:66205207-66205952	HepG2	liver:	n/a	n/a
49	MYC	chr7:66205405-66205885	MCF10A-Er-Src	breast:	n/a	n/a
50	RAD21	chr7:66205273-66206326	IMR90	lung:	n/a	chr7:66205515-66205527

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:66205542-66205592	HMEC	breast:	n/a
2	chr7:66205542-66205592	HepG2	liver:	n/a
3	chr7:66205542-66205592	PrEC	prostate:	n/a
4	chr7:66205542-66205592	HUVEC	blood vessel:	n/a
5	chr7:66205542-66205592	HRCEpiC	kidney:	n/a
6	chr7:66205542-66205592	HAEpiC	amniotic membrane:	n/a
7	chr7:66205542-66205592	BJ	skin:	n/a
8	chr7:66205542-66205592	MCF-7	breast:	n/a
9	chr7:66205542-66205592	AG04449	skin:	fetal
10	chr7:66205542-66205592	HIPEpiC	eye:	n/a
11	chr7:66205542-66205592	NB4	blood:	n/a
12	chr7:66205542-66205592	H1-hESC	embryonic stem cell:	embryo
13	chr7:66205542-66205592	SK-N-SH_RA	brain:	n/a
14	chr7:66205542-66205592	IMR90	lung:	fetal
15	chr7:66205542-66205592	HRE	kidney:	n/a
16	chr7:66205542-66205592	RPTEC	kidney:	n/a
17	chr7:66205542-66205592	A549	lung:	n/a
18	chr7:66205542-66205592	HCM	heart:	n/a
19	chr7:66205542-66205592	GM12878	blood:	n/a
20	chr7:66205542-66205592	BE2_C	brain:	n/a
21	chr7:66205542-66205592	NHBE	bronchial:	n/a
22	chr7:66205542-66205592	CMK	blood:	n/a
23	chr7:66205542-66205592	Hepatocyte	liver:	n/a
24	chr7:66205542-66205592	K562	blood:	n/a
25	chr7:66205542-66205592	Caco-2	colon:	n/a
26	chr7:66205542-66205592	GM12892	blood:	n/a
27	chr7:66205542-66205592	GM06990	blood:	n/a
28	chr7:66205542-66205592	AG09309	skin:	n/a
29	chr7:66205542-66205592	AG09319	gingival:	n/a
30	chr7:66205542-66205592	GM12891	blood:	n/a
31	chr7:66205542-66205592	HL-60	blood:	n/a
32	chr7:66205542-66205592	SAEC	small airway:	n/a
33	chr7:66205542-66205592	Hela-S3	cervix:	n/a
34	chr7:66205542-66205592	AG10803	skin:	n/a
35	chr7:66205542-66205592	ovcar-3	ovarian:	n/a
36	chr7:66205542-66205592	T-47D	breast:	n/a
37	chr7:66205542-66205592	HEK293	kidney:	embryo
38	chr7:66205542-66205592	NHDF-neo	bronchial:	n/a
39	chr7:66205542-66205592	SK-N-MC	brain:	n/a
40	chr7:66205542-66205592	HRPEpiC	eye:	n/a
41	chr7:66205542-66205592	AoSMC	blood vessel:	n/a
42	chr7:66205542-66205592	HNPCEpiC	eye:	n/a
43	chr7:66205542-66205592	HCT-116	colon:	n/a
44	chr7:66205542-66205592	PFSK-1	brain:	n/a
45	chr7:66205542-66205592	AG04450	lung:	fetal
46	chr7:66205542-66205592	HCPEpiC	choroid plexus:	n/a
47	chr7:66205542-66205592	NH-A	brain:	n/a
48	chr7:66205542-66205592	Jurkat	blood:	n/a
49	chr7:66205542-66205592	HPAEpiC	pulmonary alveolar:	n/a
50	chr7:66205542-66205592	LNCaP	prostate:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150551545..150552358-chr7:66205002..66205777,2	Hela-S3	cervix:
2	chr7:66117717..66119604-chr7:66204829..66207389,2	K562	blood:
3	chr7:66204928..66209821-chr7:66213597..66216412,7	MCF-7	breast:
4	chr7:66119315..66119930-chr7:66205425..66206247,2	NB4	blood:
5	chr7:66144687..66148625-chr7:66203954..66207507,6	K562	blood:
6	chr7:66021310..66024220-chr7:66204826..66206647,2	MCF-7	breast:
7	chr7:66119236..66121485-chr7:66204940..66206778,2	K562	blood:
8	chr7:66144717..66148625-chr7:66203954..66207507,5	K562	blood:
9	chr1:28832466..28833159-chr7:66205007..66205858,2	NB4	blood:
10	chr20:62612068..62612707-chr7:66205545..66206428,2	Hela-S3	cervix:
11	chr7:66203955..66208659-chr7:66209716..66215353,8	K562	blood:
12	chr7:66205494..66207120-chr7:66460055..66461810,2	MCF-7	breast:
13	chr7:66204784..66206359-chr7:66385620..66388278,2	MCF-7	breast:
14	chr3:50378036..50378624-chr7:66205521..66206190,2	Hela-S3	cervix:
15	chr7:66118921..66119611-chr7:66204868..66205819,2	HCT-116	colon:

Variant related genes	Relation type
RABGEF1	TF binding region
ENSG00000272831	TF binding region
KCTD7	TF binding region
ENSG00000272831	CpG island
KCTD7	CpG island
RABGEF1	CpG island
ENSG00000242125	Chromatin interaction
ENSG00000101161	Chromatin interaction
ENSG00000154710	Chromatin interaction
ENSG00000126524	Chromatin interaction
ENSG00000271064	Chromatin interaction
ENSG00000177418	Chromatin interaction
ENSG00000198874	Chromatin interaction
ENSG00000226824	Chromatin interaction
ENSG00000235058	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000106609	Chromatin interaction
ENSG00000068028	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12056129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2055683	0.81[EUR][1000 genomes]
rs3735151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9638494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	esv3401338	chr7:66147493-66206298	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv971490	chr7:66192193-66212423	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 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	chr7:66204200-66208000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr7:66204400-66205800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:66204400-66205800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr7:66204400-66207200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:66204400-66207400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr7:66204400-66207800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:66204600-66206600	Active TSS	Fetal Intestine Small	intestine
8	chr7:66204600-66206600	Active TSS	Thymus	Thymus
9	chr7:66204600-66206800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr7:66204600-66206800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr7:66204600-66206800	Active TSS	Fetal Kidney	kidney
12	chr7:66204600-66207000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr7:66204600-66207000	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr7:66204600-66207000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr7:66204600-66207000	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr7:66204600-66207000	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr7:66204600-66207000	Active TSS	Colon Smooth Muscle	Colon
18	chr7:66204600-66207000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr7:66204600-66207000	Active TSS	Psoas Muscle	Psoas
20	chr7:66204600-66207000	Active TSS	Right Ventricle	heart
21	chr7:66204600-66207200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr7:66204600-66207400	Active TSS	HMEC	breast
23	chr7:66204600-66207600	Active TSS	NHDF-Ad	bronchial
24	chr7:66204600-66207800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:66204800-66206400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr7:66204800-66206600	Active TSS	Fetal Brain Female	brain
27	chr7:66204800-66206600	Active TSS	Fetal Intestine Large	intestine
28	chr7:66204800-66206800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr7:66204800-66206800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:66204800-66206800	Active TSS	Esophagus	oesophagus
31	chr7:66204800-66206800	Active TSS	Left Ventricle	heart
32	chr7:66204800-66206800	Active TSS	Lung	lung
33	chr7:66204800-66206800	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr7:66204800-66207000	Active TSS	H9 Cell Line	embryonic stem cell
35	chr7:66204800-66207000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:66204800-66207000	Active TSS	Ovary	ovary
37	chr7:66204800-66207000	Active TSS	A549	lung
38	chr7:66204800-66207400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:66204800-66207600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:66204800-66207600	Active TSS	HSMMtube	muscle
41	chr7:66204800-66207600	Active TSS	NHLF	lung
42	chr7:66204800-66208000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:66205000-66205800	Active TSS	Fetal Heart	heart
44	chr7:66205000-66206400	Active TSS	Primary T cells from cord blood	blood
45	chr7:66205000-66206400	Active TSS	Brain Anterior Caudate	brain
46	chr7:66205000-66206600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:66205000-66206600	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr7:66205000-66206600	Active TSS	Brain Angular Gyrus	brain
49	chr7:66205000-66206600	Active TSS	Fetal Brain Male	brain
50	chr7:66205000-66206600	Active TSS	Fetal Stomach	stomach

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