Variant report

Variant	rs4457792
Chromosome Location	chr12:56109786-56109787
allele	C/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	BHLHE40	chr12:56109583-56110491	GM12878	blood:	n/a	chr12:56109825-56109834 chr12:56109826-56109835 chr12:56109810-56109819 chr12:56109824-56109837 chr12:56109827-56109836 chr12:56109810-56109819 chr12:56109820-56109841 chr12:56109808-56109821 chr12:56109826-56109835 chr12:56109811-56109820
2	CREB1	chr12:56109703-56110512	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr12:56109579-56110134	GM12891	blood:	n/a	n/a
4	IRF1	chr12:56109639-56110224	K562	blood:	n/a	chr12:56109757-56109766
5	CHD2	chr12:56109617-56110453	H1-hESC	embryonic stem cell:	n/a	n/a
6	RCOR1	chr12:56109643-56110475	K562	blood:	n/a	n/a
7	USF1	chr12:56109232-56110268	A549	lung:	n/a	chr12:56109825-56109834 chr12:56109826-56109835 chr12:56109810-56109819 chr12:56109824-56109837 chr12:56109827-56109836 chr12:56109810-56109819 chr12:56109820-56109841 chr12:56109808-56109821 chr12:56109826-56109835 chr12:56109811-56109820
8	THAP1	chr12:56109728-56109910	K562	blood:	n/a	n/a
9	BCLAF1	chr12:56109520-56110167	GM12878	blood:	n/a	n/a
10	SP1	chr12:56109541-56110108	H1-hESC	embryonic stem cell:	n/a	chr12:56109895-56109904 chr12:56109895-56109909
11	UBTF	chr12:56109683-56110520	K562	blood:	n/a	n/a
12	POLR2A	chr12:56109598-56110124	GM12891	blood:	n/a	n/a
13	USF1	chr12:56109230-56110539	ECC-1	luminal epithelium:	n/a	chr12:56109825-56109834 chr12:56109826-56109835 chr12:56109810-56109819 chr12:56109824-56109837 chr12:56109827-56109836 chr12:56109810-56109819 chr12:56109820-56109841 chr12:56109808-56109821 chr12:56109826-56109835 chr12:56109811-56109820
14	ZBTB33	chr12:56109627-56110047	A549	lung:	n/a	n/a
15	TBL1XR1	chr12:56109655-56110176	K562	blood:	n/a	n/a
16	PML	chr12:56109603-56110224	MCF-7	breast:	n/a	n/a
17	RELA	chr12:56109291-56110531	GM18951	blood:	n/a	n/a
18	NFE2	chr12:56109582-56110080	GM12878	blood:	n/a	chr12:56109814-56109829 chr12:56109826-56109835 chr12:56109824-56109833 chr12:56109810-56109819 chr12:56109815-56109824
19	POLR2A	chr12:56109542-56111672	GM12891	blood:	n/a	n/a
20	POLR2A	chr12:56109617-56110548	GM19193	blood:	n/a	n/a
21	E2F4	chr12:56109573-56110637	MCF10A-Er-Src	breast:	n/a	chr12:56110282-56110294 chr12:56110283-56110294 chr12:56109757-56109772
22	SIX5	chr12:56109350-56110313	A549	lung:	n/a	n/a
23	YY1	chr12:56109596-56110580	H1-hESC	embryonic stem cell:	n/a	chr12:56110231-56110242
24	POLR2A	chr12:56109640-56110533	GM12892	blood:	n/a	n/a
25	ATF3	chr12:56109634-56110151	K562	blood:	n/a	chr12:56109815-56109835 chr12:56109810-56109819 chr12:56109826-56109835 chr12:56109826-56109846
26	PML	chr12:56109628-56110169	GM12878	blood:	n/a	n/a
27	CEBPB	chr12:56109565-56110391	A549	lung:	n/a	n/a
28	NR2F2	chr12:56109498-56110209	MCF-7	breast:	n/a	n/a
29	MAX	chr12:56109568-56110066	H1-hESC	embryonic stem cell:	n/a	chr12:56109826-56109835 chr12:56109824-56109837 chr12:56109810-56109819 chr12:56109824-56109837 chr12:56109826-56109835 chr12:56109826-56109835
30	EP300	chr12:56109590-56110008	SK-N-SH_RA	brain:	n/a	n/a
31	USF1	chr12:56109387-56110376	H1-hESC	embryonic stem cell:	n/a	chr12:56109825-56109834 chr12:56109826-56109835 chr12:56109810-56109819 chr12:56109824-56109837 chr12:56109827-56109836 chr12:56109810-56109819 chr12:56109820-56109841 chr12:56109808-56109821 chr12:56109826-56109835 chr12:56109811-56109820
32	ELF1	chr12:56109612-56110034	HepG2	liver:	n/a	n/a
33	SIX5	chr12:56109713-56109993	GM12878	blood:	n/a	n/a
34	E2F6	chr12:56109498-56110596	A549	lung:	n/a	chr12:56110282-56110294 chr12:56109757-56109772
35	CTCF	chr12:56109752-56109883	SK-N-SH_RA	brain:	n/a	n/a
36	POLR2A	chr12:56109324-56112454	U87	brain:	n/a	n/a
37	POLR2A	chr12:56109719-56110104	Gliobla	brain:	n/a	n/a
38	EGR1	chr12:56109596-56110054	H1-hESC	embryonic stem cell:	n/a	n/a
39	E2F6	chr12:56109437-56110516	H1-hESC	embryonic stem cell:	n/a	chr12:56110282-56110294 chr12:56109757-56109772
40	POLR2A	chr12:56109503-56110589	PANC-1	pancreas:	n/a	n/a
41	ATF3	chr12:56109533-56110116	A549	lung:	n/a	chr12:56109815-56109835 chr12:56109810-56109819 chr12:56109826-56109835 chr12:56109826-56109846
42	POLR2A	chr12:56109720-56110123	MCF-7	breast:	n/a	n/a
43	TCF12	chr12:56109238-56110709	A549	lung:	n/a	chr12:56110217-56110224
44	CHD2	chr12:56109674-56110453	GM12878	blood:	n/a	n/a
45	EP300	chr12:56109682-56110645	GM12878	blood:	n/a	chr12:56110235-56110251
46	POLR2A	chr12:56109445-56110540	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr12:56109607-56110169	HepG2	liver:	n/a	n/a
48	YY1	chr12:56109587-56110122	GM12878	blood:	n/a	n/a
49	POLR2A	chr12:56109603-56110563	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr12:56109652-56110019	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:56109767-56109817	ProgFib	skin:	n/a
2	chr12:56109767-56109817	Hepatocyte	liver:	n/a
3	chr12:56109767-56109817	PFSK-1	brain:	n/a
4	chr12:56109767-56109817	NHBE	bronchial:	n/a
5	chr12:56109767-56109817	NHDF-neo	bronchial:	n/a
6	chr12:56109767-56109817	HRE	kidney:	n/a
7	chr12:56109767-56109817	AG10803	skin:	n/a
8	chr12:56109767-56109817	HRPEpiC	eye:	n/a
9	chr12:56109767-56109817	T-47D	breast:	n/a
10	chr12:56109767-56109817	H1-hESC	embryonic stem cell:	embryo
11	chr12:56109767-56109817	GM12891	blood:	n/a
12	chr12:56109767-56109817	U87	brain:	n/a
13	chr12:56109767-56109817	K562	blood:	n/a
14	chr12:56109767-56109817	MCF-7	breast:	n/a
15	chr12:56109767-56109817	HEEpiC	esophagus:	n/a
16	chr12:56109767-56109817	AG04449	skin:	fetal
17	chr12:56109767-56109817	HEK293	kidney:	embryo
18	chr12:56109767-56109817	CMK	blood:	n/a
19	chr12:56109767-56109817	NH-A	brain:	n/a
20	chr12:56109767-56109817	AoSMC	blood vessel:	n/a
21	chr12:56109767-56109817	HepG2	liver:	n/a
22	chr12:56109767-56109817	PANC-1	pancreas:	n/a
23	chr12:56109767-56109817	GM12892	blood:	n/a
24	chr12:56109767-56109817	NT2-D1	testis:	n/a
25	chr12:56109767-56109817	MCF10A-Er-Src	breast:	n/a
26	chr12:56109767-56109817	GM19239	blood:	n/a
27	chr12:56109767-56109817	ovcar-3	ovarian:	n/a
28	chr12:56109767-56109817	SK-N-SH	brain:	n/a
29	chr12:56109767-56109817	HPAEpiC	pulmonary alveolar:	n/a
30	chr12:56109767-56109817	HCF	heart:	n/a
31	chr12:56109767-56109817	Hela-S3	cervix:	n/a
32	chr12:56109767-56109817	ECC-1	luminal epithelium:	n/a
33	chr12:56109767-56109817	AG09319	gingival:	n/a
34	chr12:56109767-56109817	SKMC	muscle:	n/a
35	chr12:56109767-56109817	PrEC	prostate:	n/a
36	chr12:56109767-56109817	IMR90	lung:	fetal
37	chr12:56109767-56109817	GM12878	blood:	n/a
38	chr12:56109767-56109817	Jurkat	blood:	n/a
39	chr12:56109767-56109817	HAEpiC	amniotic membrane:	n/a
40	chr12:56109767-56109817	HCPEpiC	choroid plexus:	n/a
41	chr12:56109767-56109817	RPTEC	kidney:	n/a
42	chr12:56109767-56109817	BE2_C	brain:	n/a
43	chr12:56109767-56109817	GM06990	blood:	n/a
44	chr12:56109767-56109817	HIPEpiC	eye:	n/a
45	chr12:56109767-56109817	AG09309	skin:	n/a
46	chr12:56109767-56109817	HL-60	blood:	n/a
47	chr12:56109767-56109817	SK-N-MC	brain:	n/a
48	chr12:56109767-56109817	SK-N-SH_RA	brain:	n/a
49	chr12:56109767-56109817	HUVEC	blood vessel:	n/a
50	chr12:56109767-56109817	HMEC	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56109756..56110643-chr16:83986558..83987219,2	HCT-116	colon:
2	chr12:56108963..56111189-chr12:56554025..56556182,2	MCF-7	breast:
3	chr12:56073967..56077119-chr12:56108776..56115360,8	MCF-7	breast:
4	chr12:56105036..56107744-chr12:56108446..56111418,3	MCF-7	breast:
5	chr12:56109351..56109851-chr14:24630192..24630848,2	Hela-S3	cervix:
6	chr12:56109473..56111446-chr12:56417977..56420128,2	K562	blood:
7	chr12:56108323..56110419-chr12:56210123..56212582,2	MCF-7	breast:
8	chr12:56107674..56111560-chr12:56417665..56420637,3	MCF-7	breast:
9	chr10:91402561..91404356-chr12:56108835..56111046,2	MCF-7	breast:
10	chr12:56098605..56104708-chr12:56107025..56111403,7	MCF-7	breast:
11	chr12:30948464..30949252-chr12:56109408..56110034,2	Hela-S3	cervix:
12	chr12:56107652..56112121-chr12:56134921..56139203,6	MCF-7	breast:
13	chr12:56109642..56110298-chr3:44902738..44903430,2	Hela-S3	cervix:

Variant related genes	Relation type
ITGA7	TF binding region
BLOC1S1	TF binding region
RDH5	TF binding region
ENSG00000258311	TF binding region
ITGA7	CpG island
BLOC1S1	CpG island
RDH5	CpG island
ENSG00000258311	CpG island
ENSG00000170439	Chromatin interaction
ENSG00000140961	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000152782	Chromatin interaction
ENSG00000169964	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000235884	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000207783	Chromatin interaction
ENSG00000213928	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13193	0.80[EUR][1000 genomes]
rs1463591	0.82[CEU][hapmap]
rs2231462	0.82[CEU][hapmap]
rs73119219	0.91[EUR][1000 genomes]
rs7959622	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv525231	chr12:56076919-56124332	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
4	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 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	chr12:56109000-56109800	Flanking Active TSS	Colon Smooth Muscle	Colon
2	chr12:56109000-56109800	Flanking Active TSS	Dnd41	blood
3	chr12:56109000-56109800	Flanking Active TSS	Hela-S3	cervix
4	chr12:56109000-56110000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:56109000-56111400	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr12:56109000-56111600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr12:56109000-56115600	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr12:56109200-56109800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:56109200-56109800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:56109200-56109800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr12:56109200-56109800	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr12:56109200-56109800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:56109200-56109800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr12:56109200-56109800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr12:56109200-56109800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:56109200-56109800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:56109200-56109800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr12:56109200-56109800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:56109200-56109800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:56109200-56109800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:56109200-56109800	Flanking Active TSS	Liver	Liver
22	chr12:56109200-56109800	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr12:56109200-56109800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:56109200-56109800	Flanking Active TSS	Colonic Mucosa	Colon
25	chr12:56109200-56109800	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr12:56109200-56109800	Flanking Active TSS	Fetal Brain Male	brain
27	chr12:56109200-56109800	Flanking Active TSS	Fetal Brain Female	brain
28	chr12:56109200-56109800	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr12:56109200-56109800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr12:56109200-56109800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr12:56109200-56109800	Enhancers	Spleen	Spleen
32	chr12:56109200-56109800	Flanking Active TSS	A549	lung
33	chr12:56109200-56109800	Flanking Active TSS	HSMMtube	muscle
34	chr12:56109200-56109800	Flanking Active TSS	K562	blood
35	chr12:56109200-56109800	Flanking Active TSS	NHDF-Ad	bronchial
36	chr12:56109200-56109800	Flanking Active TSS	NHEK	skin
37	chr12:56109200-56109800	Flanking Active TSS	NHLF	lung
38	chr12:56109200-56109800	Flanking Active TSS	Osteobl	bone
39	chr12:56109200-56110000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:56109200-56110600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:56109200-56110800	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:56109200-56110800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:56109200-56110800	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr12:56109200-56111200	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr12:56109200-56111400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:56109200-56111400	Flanking Active TSS	Fetal Muscle Trunk	muscle
47	chr12:56109200-56112200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr12:56109400-56109800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr12:56109400-56109800	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr12:56109400-56109800	Flanking Active TSS	Primary hematopoietic stem cells	blood

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