Variant report

Variant	rs189195538
Chromosome Location	chr12:50479577-50479578
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	chr12:50478628-50479735	H1-neurons	neurons:	n/a	n/a
2	SIN3A	chr12:50478566-50479817	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr12:50478577-50479638	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr12:50478666-50479590	HepG2	liver:	n/a	n/a
5	EBF1	chr12:50479260-50479968	GM12878	blood:	n/a	chr12:50479421-50479431 chr12:50479420-50479433 chr12:50479422-50479431 chr12:50479422-50479431 chr12:50479520-50479531 chr12:50479519-50479532 chr12:50479521-50479531 chr12:50479521-50479530 chr12:50479521-50479530
6	POLR2A	chr12:50477999-50480078	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:50478620-50479711	K562	blood:	n/a	n/a
8	POLR2A	chr12:50478434-50480257	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAZ	chr12:50478459-50480271	IMR90	lung:	n/a	chr12:50478768-50478777
10	CHD1	chr12:50478135-50479792	IMR90	lung:	n/a	n/a
11	MXI1	chr12:50478105-50480000	SK-N-SH	brain:	n/a	n/a
12	MYC	chr12:50478606-50479653	A549	lung:	n/a	chr12:50478768-50478777
13	CTCF	chr12:50479500-50479650	AG09319	gingival:	n/a	n/a
14	RFX5	chr12:50478473-50479811	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr12:50478514-50479611	Hela-S3	cervix:	n/a	n/a
16	ZBTB7A	chr12:50478654-50479637	K562	blood:	n/a	n/a
17	POLR2A	chr12:50478568-50479789	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr12:50478485-50479655	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr12:50478459-50479959	HUVEC	blood vessel:	n/a	n/a
20	EBF1	chr12:50479225-50479685	GM12878	blood:	n/a	chr12:50479421-50479431 chr12:50479420-50479433 chr12:50479422-50479431 chr12:50479422-50479431 chr12:50479520-50479531 chr12:50479519-50479532 chr12:50479521-50479531 chr12:50479521-50479530 chr12:50479521-50479530
21	MAZ	chr12:50478652-50479613	K562	blood:	n/a	chr12:50478768-50478777
22	MAZ	chr12:50478662-50479725	HepG2	liver:	n/a	chr12:50478768-50478777
23	POLR2A	chr12:50478662-50479608	GM18951	blood:	n/a	n/a
24	MAZ	chr12:50478597-50479690	GM12878	blood:	n/a	chr12:50478768-50478777
25	POLR2A	chr12:50478472-50479702	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr12:50478486-50479801	K562	blood:	n/a	n/a
27	HCFC1	chr12:50478275-50480063	Hela-S3	cervix:	n/a	n/a
28	TAF1	chr12:50478467-50479715	ECC-1	luminal epithelium:	n/a	n/a
29	EBF1	chr12:50479289-50479725	GM12878	blood:	n/a	chr12:50479421-50479431 chr12:50479420-50479433 chr12:50479422-50479431 chr12:50479422-50479431 chr12:50479520-50479531 chr12:50479519-50479532 chr12:50479521-50479531 chr12:50479521-50479530 chr12:50479521-50479530
30	TCF12	chr12:50478379-50479603	A549	lung:	n/a	n/a
31	POLR2A	chr12:50478714-50479741	MCF-7	breast:	n/a	n/a
32	POLR2A	chr12:50479566-50479784	MCF10A-Er-Src	breast:	n/a	n/a
33	TCF12	chr12:50478487-50479590	ECC-1	luminal epithelium:	n/a	n/a
34	MTA3	chr12:50478397-50479798	GM12878	blood:	n/a	n/a
35	POLR2A	chr12:50478553-50479670	GM12878	blood:	n/a	n/a
36	POLR2A	chr12:50478485-50479868	GM12878	blood:	n/a	n/a
37	REST	chr12:50478417-50480009	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr12:50478555-50479685	Raji	blood:	n/a	n/a
39	MAX	chr12:50478396-50479594	A549	lung:	n/a	chr12:50478768-50478777
40	IRF1	chr12:50478726-50479641	K562	blood:	n/a	chr12:50479110-50479123 chr12:50478970-50478984
41	PBX3	chr12:50478668-50479632	SK-N-SH	brain:	n/a	n/a
42	ZBTB7A	chr12:50478495-50479756	ECC-1	luminal epithelium:	n/a	n/a
43	TCF12	chr12:50478592-50479838	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr12:50478497-50479667	HepG2	liver:	n/a	n/a
45	ZBTB7A	chr12:50478469-50479765	ECC-1	luminal epithelium:	n/a	n/a
46	CHD2	chr12:50478568-50479715	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50477150..50481052-chr12:50559881..50562931,6	MCF-7	breast:
2	chr12:50478595..50483647-chr12:50502911..50507517,7	K562	blood:
3	chr12:50478513..50480166-chr12:50489047..50490966,2	K562	blood:
4	chr12:50466696..50474949-chr12:50474970..50481457,17	MCF-7	breast:
5	chr12:50472028..50474859-chr12:50477717..50480636,3	MCF-7	breast:
6	chr12:50477580..50479686-chr17:62501151..62502654,2	MCF-7	breast:
7	chr12:50478149..50480392-chr17:58677532..58679268,2	MCF-7	breast:
8	chr12:50477670..50481382-chr12:50495555..50500836,7	K562	blood:
9	chr12:50478449..50481902-chr12:50536030..50539935,3	MCF-7	breast:
10	chr12:50475132..50479699-chr12:50479828..50484275,5	K562	blood:
11	chr12:50477885..50480264-chr12:50559751..50562542,2	K562	blood:
12	chr12:50478759..50480659-chr12:50481009..50483998,3	K562	blood:
13	chr12:50135082..50136603-chr12:50479268..50481708,2	MCF-7	breast:
14	chr12:50475972..50484033-chr12:50500850..50507517,14	K562	blood:
15	chr12:50477567..50484756-chr12:50559008..50565131,16	MCF-7	breast:
16	chr12:49524766..49526462-chr12:50478450..50480251,2	MCF-7	breast:
17	chr12:50477688..50480373-chr12:50497434..50499573,3	K562	blood:
18	chr12:50478705..50480450-chr12:50534679..50536447,2	MCF-7	breast:
19	chr12:50477178..50480105-chr12:50648113..50650406,2	K562	blood:
20	chr12:50235441..50237993-chr12:50478392..50480338,2	K562	blood:
21	chr12:50464456..50466840-chr12:50477683..50480596,2	MCF-7	breast:

Variant related genes	Relation type
SMARCD1	TF binding region
ENSG00000170836	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000167588	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000212496	Chromatin interaction
ENSG00000139624	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	esv3437172	chr12:50478110-50480658	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 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	chr12:50478000-50479600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr12:50478000-50480200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:50478200-50479600	Active TSS	Aorta	Aorta
4	chr12:50478200-50479600	Active TSS	Colonic Mucosa	Colon
5	chr12:50478200-50479600	Active TSS	Colon Smooth Muscle	Colon
6	chr12:50478200-50479600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr12:50478200-50479600	Active TSS	Pancreas	Pancrea
8	chr12:50478200-50479600	Active TSS	A549	lung
9	chr12:50478200-50479600	Active TSS	HepG2	liver
10	chr12:50478200-50479600	Active TSS	HMEC	breast
11	chr12:50478200-50479600	Active TSS	HSMM	muscle
12	chr12:50478200-50479600	Active TSS	HSMMtube	muscle
13	chr12:50478200-50479800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr12:50478200-50479800	Active TSS	Fetal Lung	lung
15	chr12:50478200-50479800	Active TSS	Left Ventricle	heart
16	chr12:50478200-50479800	Active TSS	Right Atrium	heart
17	chr12:50478200-50479800	Active TSS	Stomach Smooth Muscle	stomach
18	chr12:50478200-50479800	Active TSS	GM12878-XiMat	blood
19	chr12:50478200-50479800	Active TSS	NHEK	skin
20	chr12:50478200-50480000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr12:50478200-50480000	Active TSS	Fetal Brain Female	brain
22	chr12:50478200-50480000	Active TSS	Fetal Kidney	kidney
23	chr12:50478200-50480000	Active TSS	Psoas Muscle	Psoas
24	chr12:50478200-50480200	Active TSS	H9 Cell Line	embryonic stem cell
25	chr12:50478200-50480200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:50478200-50480200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:50478200-50480200	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr12:50478200-50480200	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr12:50478200-50480200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:50478200-50480200	Active TSS	Rectal Smooth Muscle	rectum
31	chr12:50478200-50480200	Active TSS	NHLF	lung
32	chr12:50478200-50480400	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr12:50478400-50479600	Active TSS	H1 Cell Line	embryonic stem cell
34	chr12:50478400-50479600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:50478400-50479600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:50478400-50479600	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr12:50478400-50479600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr12:50478400-50479600	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr12:50478400-50479600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:50478400-50479600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:50478400-50479600	Active TSS	Brain Hippocampus Middle	brain
42	chr12:50478400-50479600	Active TSS	Fetal Heart	heart
43	chr12:50478400-50479600	Active TSS	Fetal Stomach	stomach
44	chr12:50478400-50479600	Active TSS	Ovary	ovary
45	chr12:50478400-50479600	Active TSS	Right Ventricle	heart
46	chr12:50478400-50479600	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr12:50478400-50479600	Active TSS	Thymus	Thymus
48	chr12:50478400-50479600	Active TSS	K562	blood
49	chr12:50478400-50479800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr12:50478400-50479800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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