Variant report

Variant	rs4996382
Chromosome Location	chr12:56754466-56754467
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	chr12:56753532-56754597	K562	blood:	n/a	n/a
2	NFIC	chr12:56753688-56754815	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:56753568-56754634	HUVEC	blood vessel:	n/a	n/a
4	MAX	chr12:56753559-56754574	ECC-1	luminal epithelium:	n/a	chr12:56753860-56753870
5	POLR2A	chr12:56754160-56754548	SK-N-SH	brain:	n/a	n/a
6	GABPA	chr12:56753584-56754737	SK-N-SH	brain:	n/a	chr12:56753859-56753868
7	SRF	chr12:56753610-56754504	ECC-1	luminal epithelium:	n/a	chr12:56753860-56753870
8	CCNT2	chr12:56753631-56754466	K562	blood:	n/a	chr12:56753803-56753812 chr12:56753808-56753817
9	TEAD4	chr12:56753682-56754689	ECC-1	luminal epithelium:	n/a	n/a
10	YY1	chr12:56754124-56754667	A549	lung:	n/a	n/a
11	YY1	chr12:56753686-56754530	SK-N-SH	brain:	n/a	n/a
12	PML	chr12:56753580-56754517	K562	blood:	n/a	n/a
13	ETS1	chr12:56753711-56754487	A549	lung:	n/a	chr12:56753983-56753992
14	TAF1	chr12:56753580-56754494	GM12878	blood:	n/a	n/a
15	SRF	chr12:56753732-56754521	MCF-7	breast:	n/a	chr12:56753860-56753870
16	TAF1	chr12:56753679-56754483	PFSK-1	brain:	n/a	n/a
17	ATF2	chr12:56753723-56754529	GM12878	blood:	n/a	n/a
18	GABPA	chr12:56753726-56754519	HL-60	blood:	n/a	chr12:56753859-56753868
19	ELF1	chr12:56753649-56754560	SK-N-SH	brain:	n/a	chr12:56753979-56753992
20	EP300	chr12:56753899-56754531	A549	lung:	n/a	chr12:56754072-56754081
21	GABPA	chr12:56753685-56754632	MCF-7	breast:	n/a	chr12:56753859-56753868
22	YY1	chr12:56753516-56754535	ECC-1	luminal epithelium:	n/a	n/a
23	CHD1	chr12:56754194-56754687	H1-hESC	embryonic stem cell:	n/a	n/a
24	RELA	chr12:56753677-56754617	GM15510	blood:	n/a	n/a
25	TCF12	chr12:56753771-56754477	A549	lung:	n/a	chr12:56754252-56754259
26	POLR2A	chr12:56753581-56754532	K562	blood:	n/a	n/a
27	HA-E2F1	chr12:56753901-56754548	MCF-7	breast:	n/a	n/a
28	POLR2A	chr12:56754105-56754584	Hela-S3	cervix:	n/a	n/a
29	TRIM28	chr12:56753566-56754506	K562	blood:	n/a	n/a
30	RUNX3	chr12:56753542-56754482	GM12878	blood:	n/a	n/a
31	YY1	chr12:56753760-56754478	HCT-116	colon:	n/a	n/a
32	NR2F2	chr12:56753994-56754726	K562	blood:	n/a	n/a
33	RUNX3	chr12:56753512-56754474	GM12878	blood:	n/a	n/a
34	SP1	chr12:56753481-56754742	H1-hESC	embryonic stem cell:	n/a	chr12:56753960-56753972 chr12:56754296-56754310 chr12:56753802-56753816 chr12:56754097-56754108 chr12:56753961-56753971 chr12:56754083-56754094 chr12:56753961-56753970 chr12:56753960-56753972 chr12:56754083-56754095
35	TBL1XR1	chr12:56753546-56754507	K562	blood:	n/a	n/a
36	YY1	chr12:56753675-56754674	GM12878	blood:	n/a	n/a
37	SIX5	chr12:56754067-56754467	A549	lung:	n/a	n/a
38	MXI1	chr12:56752439-56754755	IMR90	lung:	n/a	n/a
39	MAX	chr12:56753665-56754580	SK-N-SH	brain:	n/a	chr12:56753860-56753870
40	NFIC	chr12:56753957-56754517	HepG2	liver:	n/a	n/a
41	POU2F2	chr12:56753604-56754603	GM12878	blood:	n/a	n/a
42	NR2F2	chr12:56753462-56754894	K562	blood:	n/a	n/a
43	TAF1	chr12:56753556-56754609	ECC-1	luminal epithelium:	n/a	n/a
44	MAX	chr12:56753633-56754509	H1-hESC	embryonic stem cell:	n/a	chr12:56753860-56753870
45	ELF1	chr12:56753566-56754519	GM12878	blood:	n/a	chr12:56753979-56753992
46	POLR2A	chr12:56753427-56754724	K562	blood:	n/a	n/a
47	CREB1	chr12:56753827-56754562	ECC-1	luminal epithelium:	n/a	n/a
48	TCF12	chr12:56753405-56755077	ECC-1	luminal epithelium:	n/a	chr12:56754252-56754259
49	GABPA	chr12:56753345-56754969	MCF-7	breast:	n/a	chr12:56753859-56753868
50	E2F6	chr12:56753761-56754573	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56710034..56711597-chr12:56754145..56755894,2	K562	blood:
2	chr12:56748050..56751002-chr12:56753460..56756305,2	K562	blood:
3	chr12:56707405..56709200-chr12:56752769..56755378,2	MCF-7	breast:
4	chr12:56752493..56755436-chr12:56859728..56862331,2	MCF-7	breast:
5	chr12:56752523..56755343-chr12:56862151..56864248,2	MCF-7	breast:
6	chr12:56752238..56754707-chr12:56756251..56758252,3	MCF-7	breast:
7	chr12:56743017..56746738-chr12:56752337..56755444,3	K562	blood:
8	chr12:56727184..56732099-chr12:56751309..56755132,9	K562	blood:
9	chr12:56753830..56756625-chr12:57028420..57030715,2	MCF-7	breast:
10	chr12:56726570..56729841-chr12:56754004..56757409,3	MCF-7	breast:
11	chr12:56725978..56729877-chr12:56750632..56755261,5	MCF-7	breast:
12	chr12:56747914..56751304-chr12:56752091..56755313,3	MCF-7	breast:
13	chr12:56694141..56695948-chr12:56754133..56756336,2	MCF-7	breast:
14	chr12:56753916..56755760-chr12:56841528..56845904,3	K562	blood:
15	chr12:56716783..56718738-chr12:56753948..56755499,2	K562	blood:
16	chr12:56582084..56583845-chr12:56753291..56755155,2	MCF-7	breast:
17	chr12:56582392..56584464-chr12:56753681..56756139,2	MCF-7	breast:
18	chr12:56721052..56723021-chr12:56754281..56756582,2	MCF-7	breast:
19	chr12:56753203..56755632-chr12:56841567..56843289,3	MCF-7	breast:

Variant related genes	Relation type
STAT2	TF binding region
ENSG00000135517	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000111602	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000252206	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000175336	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11575221	0.82[AMR][1000 genomes]
rs11575236	0.82[AMR][1000 genomes]
rs1918496	0.82[AMR][1000 genomes]
rs4301822	0.86[AMR][1000 genomes]
rs73324336	0.82[AMR][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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 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	chr12:56751600-56755000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:56751600-56755000	Active TSS	GM12878-XiMat	blood
3	chr12:56752000-56754800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:56752200-56755000	Active TSS	HSMMtube	muscle
5	chr12:56752400-56754800	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr12:56752400-56754800	Active TSS	Sigmoid Colon	Sigmoid Colon
7	chr12:56752400-56755000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr12:56752400-56755200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr12:56752400-56755200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:56752400-56755200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr12:56752400-56755600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:56752600-56754600	Active TSS	Fetal Muscle Trunk	muscle
13	chr12:56752600-56754800	Active TSS	Aorta	Aorta
14	chr12:56752600-56755000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:56752600-56755000	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:56752600-56755200	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:56752800-56754600	Active TSS	HepG2	liver
18	chr12:56752800-56754800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:56752800-56754800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:56752800-56754800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:56752800-56754800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:56752800-56754800	Active TSS	Colonic Mucosa	Colon
23	chr12:56752800-56754800	Active TSS	Lung	lung
24	chr12:56752800-56754800	Active TSS	Ovary	ovary
25	chr12:56752800-56754800	Active TSS	Right Atrium	heart
26	chr12:56752800-56754800	Active TSS	NHLF	lung
27	chr12:56752800-56755000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:56752800-56755000	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr12:56752800-56755000	Active TSS	Fetal Kidney	kidney
30	chr12:56752800-56755000	Active TSS	Psoas Muscle	Psoas
31	chr12:56752800-56755000	Active TSS	HSMM	muscle
32	chr12:56752800-56755000	Active TSS	NHDF-Ad	bronchial
33	chr12:56752800-56755200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:56753000-56754600	Active TSS	Small Intestine	intestine
35	chr12:56753000-56754800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:56753000-56754800	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr12:56753000-56754800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:56753000-56754800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:56753000-56754800	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr12:56753000-56754800	Active TSS	K562	blood
41	chr12:56753000-56755000	Active TSS	H1 Cell Line	embryonic stem cell
42	chr12:56753000-56755000	Active TSS	H9 Cell Line	embryonic stem cell
43	chr12:56753000-56755600	Active TSS	Brain Anterior Caudate	brain
44	chr12:56753200-56754600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:56753200-56754600	Active TSS	Primary T cells fromperipheralblood	blood
46	chr12:56753200-56754600	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr12:56753200-56754600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:56753200-56754600	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr12:56753200-56754600	Active TSS	Brain Cingulate Gyrus	brain
50	chr12:56753200-56754600	Active TSS	Brain Hippocampus Middle	brain

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