Variant report

Variant	rs7970054
Chromosome Location	chr12:59314712-59314713
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	NFIC	chr12:59313891-59314793	ECC-1	luminal epithelium:	n/a	n/a
2	MXI1	chr12:59312927-59314729	Hela-S3	cervix:	n/a	n/a
3	E2F6	chr12:59313149-59314852	H1-hESC	embryonic stem cell:	n/a	chr12:59313711-59313720 chr12:59314368-59314382
4	USF2	chr12:59314254-59314766	GM12878	blood:	n/a	chr12:59314427-59314443 chr12:59314382-59314398 chr12:59314408-59314419
5	TCF12	chr12:59313833-59314837	ECC-1	luminal epithelium:	n/a	chr12:59314210-59314217
6	ZKSCAN1	chr12:59313860-59314748	Hela-S3	cervix:	n/a	n/a
7	E2F4	chr12:59313684-59314976	MCF10A-Er-Src	breast:	n/a	chr12:59313711-59313720 chr12:59314368-59314382
8	MAZ	chr12:59313373-59314775	IMR90	lung:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
9	USF1	chr12:59313976-59314861	HCT-116	colon:	n/a	chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
10	MAX	chr12:59313222-59314799	HCT-116	colon:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
11	MXI1	chr12:59312803-59315453	IMR90	lung:	n/a	n/a
12	MAX	chr12:59312924-59314843	A549	lung:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
13	TCF12	chr12:59313290-59314748	ECC-1	luminal epithelium:	n/a	chr12:59314210-59314217
14	MAZ	chr12:59314275-59314771	GM12878	blood:	n/a	chr12:59314410-59314419 chr12:59314408-59314421 chr12:59314409-59314420 chr12:59314410-59314419
15	USF1	chr12:59313853-59314775	ECC-1	luminal epithelium:	n/a	chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
16	MYBL2	chr12:59313939-59314814	HepG2	liver:	n/a	n/a
17	USF1	chr12:59314108-59314732	A549	lung:	n/a	chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
18	CHD2	chr12:59313053-59314966	Hela-S3	cervix:	n/a	chr12:59313753-59313763
19	MAX	chr12:59313319-59314757	HCT-116	colon:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
20	E2F6	chr12:59313852-59314839	A549	lung:	n/a	chr12:59314368-59314382
21	USF1	chr12:59313331-59314861	ECC-1	luminal epithelium:	n/a	chr12:59313737-59313753 chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
22	MYC	chr12:59313125-59314869	MCF10A-Er-Src	breast:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
23	MYC	chr12:59314220-59314810	MCF10A-Er-Src	breast:	n/a	chr12:59314410-59314419 chr12:59314408-59314421 chr12:59314409-59314420 chr12:59314410-59314419
24	MAX	chr12:59313290-59314985	ECC-1	luminal epithelium:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
25	USF2	chr12:59314208-59314818	Hela-S3	cervix:	n/a	chr12:59314427-59314443 chr12:59314382-59314398 chr12:59314408-59314419
26	MAX	chr12:59313398-59314859	A549	lung:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
27	USF1	chr12:59313737-59314730	HCT-116	colon:	n/a	chr12:59313737-59313753 chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
28	KAP1	chr12:59314027-59314904	HEK293	kidney:	n/a	n/a
29	POLR2A	chr12:59309378-59314838	MCF10A-Er-Src	breast:	n/a	n/a
30	HA-E2F1	chr12:59313054-59314781	MCF-7	breast:	n/a	chr12:59313711-59313720 chr12:59314368-59314382
31	SMC3	chr12:59312951-59314846	Hela-S3	cervix:	n/a	n/a
32	MAX	chr12:59313204-59314771	HepG2	liver:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
33	MAX	chr12:59313201-59314757	A549	lung:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
34	USF1	chr12:59314037-59314734	A549	lung:	n/a	chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
35	GTF2F1	chr12:59314084-59314866	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr12:59312840-59314844	HUVEC	blood vessel:	n/a	n/a
37	TAF1	chr12:59313577-59314814	ECC-1	luminal epithelium:	n/a	n/a
38	MYC	chr12:59313338-59314855	A549	lung:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
39	NFIC	chr12:59313207-59314737	ECC-1	luminal epithelium:	n/a	n/a
40	USF1	chr12:59314012-59314736	SK-N-SH	brain:	n/a	chr12:59314409-59314420 chr12:59314427-59314443 chr12:59314382-59314398
41	POLR2A	chr12:59313133-59314758	PFSK-1	brain:	n/a	n/a
42	KAP1	chr12:59314056-59314724	U2OS	brain:	n/a	n/a
43	MAZ	chr12:59314023-59315188	HepG2	liver:	n/a	chr12:59314410-59314419 chr12:59314408-59314421 chr12:59314409-59314420 chr12:59314410-59314419
44	MAX	chr12:59313071-59314828	ECC-1	luminal epithelium:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
45	EP300	chr12:59313518-59314783	ECC-1	luminal epithelium:	n/a	chr12:59314564-59314573 chr12:59314052-59314068 chr12:59314457-59314471 chr12:59313579-59313588
46	TCF12	chr12:59313030-59314743	A549	lung:	n/a	chr12:59314210-59314217

No.	Distal block	Cell Line	Cell type
1	chr12:59306615..59312160-chr12:59312563..59315284,9	MCF-7	breast:
2	chr12:59308294..59310452-chr12:59314472..59316153,2	K562	blood:
3	chr12:59313255..59314867-chr6:27838598..27840298,2	MCF-7	breast:

Variant related genes	Relation type
LRIG3	TF binding region
ENSG00000182572	Chromatin interaction
ENSG00000139263	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10877188	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10877198	0.83[EUR][1000 genomes]
rs11172823	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172824	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172825	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172827	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11172831	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11172833	0.94[EUR][1000 genomes]
rs11172837	0.84[EUR][1000 genomes]
rs11172839	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172840	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172846	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172857	0.84[EUR][1000 genomes]
rs11172858	0.83[EUR][1000 genomes]
rs11172860	0.83[EUR][1000 genomes]
rs11172861	0.83[EUR][1000 genomes]
rs11172862	0.83[EUR][1000 genomes]
rs11172868	0.80[EUR][1000 genomes]
rs12368752	0.84[EUR][1000 genomes]
rs12370522	0.84[AMR][1000 genomes]
rs12423502	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12424788	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12426212	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12426969	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58692617	0.82[EUR][1000 genomes]
rs60522760	0.84[EUR][1000 genomes]
rs60984323	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61754220	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61919461	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61919462	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61919464	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61919465	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61919466	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61919469	0.84[EUR][1000 genomes]
rs61919471	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61919513	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61919518	0.84[EUR][1000 genomes]
rs61919519	0.84[EUR][1000 genomes]
rs61919520	0.83[EUR][1000 genomes]
rs61919521	0.84[EUR][1000 genomes]
rs61919523	0.84[EUR][1000 genomes]
rs61919524	0.83[EUR][1000 genomes]
rs61919525	0.83[EUR][1000 genomes]
rs61919531	0.82[EUR][1000 genomes]
rs61919532	0.82[EUR][1000 genomes]
rs6581224	0.83[EUR][1000 genomes]
rs7136193	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7138401	0.84[EUR][1000 genomes]
rs7294684	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7297094	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7301299	0.84[EUR][1000 genomes]
rs7302365	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7303773	0.83[EUR][1000 genomes]
rs7309872	0.84[EUR][1000 genomes]
rs7963207	0.84[EUR][1000 genomes]
rs7968111	0.83[EUR][1000 genomes]
rs7969722	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7980136	0.94[EUR][1000 genomes]
rs7980483	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9645802	0.90[AMR][1000 genomes];0.94[EUR][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	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59309200-59314800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:59309200-59314800	Active TSS	Ovary	ovary
3	chr12:59309200-59315200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr12:59309400-59315000	Active TSS	Fetal Muscle Trunk	muscle
5	chr12:59310000-59315000	Active TSS	Fetal Intestine Large	intestine
6	chr12:59310000-59315200	Active TSS	Rectal Smooth Muscle	rectum
7	chr12:59310400-59314800	Active TSS	Psoas Muscle	Psoas
8	chr12:59310400-59315200	Active TSS	Stomach Mucosa	stomach
9	chr12:59310600-59314800	Active TSS	Right Atrium	heart
10	chr12:59310600-59315000	Active TSS	Fetal Kidney	kidney
11	chr12:59310800-59314800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:59310800-59314800	Active TSS	Aorta	Aorta
13	chr12:59310800-59315000	Active TSS	Pancreas	Pancrea
14	chr12:59311000-59314800	Active TSS	Colon Smooth Muscle	Colon
15	chr12:59311000-59314800	Active TSS	Right Ventricle	heart
16	chr12:59311000-59315000	Active TSS	Colonic Mucosa	Colon
17	chr12:59311200-59314800	Active TSS	HSMM	muscle
18	chr12:59311800-59314800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:59311800-59314800	Bivalent/Poised TSS	Fetal Thymus	thymus
20	chr12:59312000-59314800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:59312000-59315000	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr12:59312000-59315200	Active TSS	Brain Anterior Caudate	brain
23	chr12:59312200-59314800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:59312200-59314800	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr12:59312200-59315000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr12:59312600-59314800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:59312600-59314800	Active TSS	A549	lung
28	chr12:59313200-59314800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:59313200-59314800	Active TSS	Placenta Amnion	Placenta Amnion
30	chr12:59313200-59315000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:59313400-59317200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:59313600-59314800	Active TSS	H1 Cell Line	embryonic stem cell
33	chr12:59313600-59314800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr12:59313600-59315000	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr12:59313600-59315000	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr12:59313800-59314800	Active TSS	Placenta	Placenta
37	chr12:59314000-59314800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
38	chr12:59314000-59314800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:59314000-59315000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
40	chr12:59314200-59314800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:59314200-59315000	Active TSS	Fetal Brain Female	brain
42	chr12:59314200-59315000	Enhancers	Fetal Heart	heart
43	chr12:59314400-59314800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:59314400-59314800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
45	chr12:59314400-59314800	Flanking Active TSS	Fetal Brain Male	brain
46	chr12:59314400-59314800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr12:59314400-59314800	Weak transcription	Spleen	Spleen
48	chr12:59314400-59314800	Flanking Active TSS	NH-A	brain
49	chr12:59314400-59315000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr12:59314400-59315000	Flanking Active TSS	Liver	Liver

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