Variant report

Variant	rs543420481
Chromosome Location	chr12:50479749-50479750
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr12:50478566-50479817	H1-hESC	embryonic stem cell:	n/a	n/a
2	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
3	POLR2A	chr12:50477999-50480078	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:50478434-50480257	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAZ	chr12:50478459-50480271	IMR90	lung:	n/a	chr12:50478768-50478777
6	CHD1	chr12:50478135-50479792	IMR90	lung:	n/a	n/a
7	MXI1	chr12:50478105-50480000	SK-N-SH	brain:	n/a	n/a
8	RFX5	chr12:50478473-50479811	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr12:50478568-50479789	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr12:50478459-50479959	HUVEC	blood vessel:	n/a	n/a
11	CTCF	chr12:50479740-50479890	HRE	kidney:	n/a	n/a
12	STAT5A	chr12:50479611-50479978	GM12878	blood:	n/a	n/a
13	E2F4	chr12:50479718-50479803	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr12:50478486-50479801	K562	blood:	n/a	n/a
15	HCFC1	chr12:50478275-50480063	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:50479566-50479784	MCF10A-Er-Src	breast:	n/a	n/a
17	MTA3	chr12:50478397-50479798	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:50478485-50479868	GM12878	blood:	n/a	n/a
19	REST	chr12:50478417-50480009	H1-neurons	neurons:	n/a	n/a
20	ZBTB7A	chr12:50478495-50479756	ECC-1	luminal epithelium:	n/a	n/a
21	TCF12	chr12:50478592-50479838	ECC-1	luminal epithelium:	n/a	n/a
22	ZBTB7A	chr12:50478469-50479765	ECC-1	luminal epithelium:	n/a	n/a
23	IRF1	chr12:50479634-50479782	K562	blood:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50479656..50481335-chr12:50569381..50571958,2	MCF-7	breast:
2	chr12:50477150..50481052-chr12:50559881..50562931,6	MCF-7	breast:
3	chr12:50478595..50483647-chr12:50502911..50507517,7	K562	blood:
4	chr12:50478513..50480166-chr12:50489047..50490966,2	K562	blood:
5	chr12:50466696..50474949-chr12:50474970..50481457,17	MCF-7	breast:
6	chr12:50472028..50474859-chr12:50477717..50480636,3	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	chr12:50477885..50480264-chr12:50559751..50562542,2	K562	blood:
11	chr12:50478759..50480659-chr12:50481009..50483998,3	K562	blood:
12	chr12:50135082..50136603-chr12:50479268..50481708,2	MCF-7	breast:
13	chr12:50475972..50484033-chr12:50500850..50507517,14	K562	blood:
14	chr12:50477567..50484756-chr12:50559008..50565131,16	MCF-7	breast:
15	chr12:49524766..49526462-chr12:50478450..50480251,2	MCF-7	breast:
16	chr12:50477688..50480373-chr12:50497434..50499573,3	K562	blood:
17	chr12:50478705..50480450-chr12:50534679..50536447,2	MCF-7	breast:
18	chr12:50477178..50480105-chr12:50648113..50650406,2	K562	blood:
19	chr12:50235441..50237993-chr12:50478392..50480338,2	K562	blood:
20	chr12:50464456..50466840-chr12:50477683..50480596,2	MCF-7	breast:

No data

Variant related genes	Relation type
SMARCD1	TF binding region
ENSG00000212496	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000167588	Chromatin interaction
ENSG00000170836	Chromatin interaction
ENSG00000066117	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	chr12:50478000-50480200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:50478200-50479800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:50478200-50479800	Active TSS	Fetal Lung	lung
4	chr12:50478200-50479800	Active TSS	Left Ventricle	heart
5	chr12:50478200-50479800	Active TSS	Right Atrium	heart
6	chr12:50478200-50479800	Active TSS	Stomach Smooth Muscle	stomach
7	chr12:50478200-50479800	Active TSS	GM12878-XiMat	blood
8	chr12:50478200-50479800	Active TSS	NHEK	skin
9	chr12:50478200-50480000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:50478200-50480000	Active TSS	Fetal Brain Female	brain
11	chr12:50478200-50480000	Active TSS	Fetal Kidney	kidney
12	chr12:50478200-50480000	Active TSS	Psoas Muscle	Psoas
13	chr12:50478200-50480200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr12:50478200-50480200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:50478200-50480200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:50478200-50480200	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr12:50478200-50480200	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr12:50478200-50480200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:50478200-50480200	Active TSS	Rectal Smooth Muscle	rectum
20	chr12:50478200-50480200	Active TSS	NHLF	lung
21	chr12:50478200-50480400	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr12:50478400-50479800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr12:50478400-50479800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:50478400-50479800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:50478400-50479800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:50478400-50479800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:50478400-50479800	Active TSS	Duodenum Mucosa	Duodenum
28	chr12:50478400-50479800	Active TSS	Esophagus	oesophagus
29	chr12:50478400-50479800	Active TSS	Fetal Intestine Large	intestine
30	chr12:50478400-50479800	Active TSS	Lung	lung
31	chr12:50478400-50479800	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr12:50478400-50479800	Active TSS	NHDF-Ad	bronchial
33	chr12:50478400-50480200	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr12:50478400-50480200	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr12:50478400-50480400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:50478400-50480600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:50478600-50479800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:50478600-50479800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:50478600-50479800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:50478600-50479800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr12:50478600-50479800	Active TSS	Fetal Brain Male	brain
42	chr12:50478600-50479800	Active TSS	Fetal Intestine Small	intestine
43	chr12:50478600-50479800	Active TSS	Gastric	stomach
44	chr12:50478600-50480200	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr12:50478800-50479800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:50478800-50479800	Active TSS	Brain Anterior Caudate	brain
47	chr12:50478800-50479800	Active TSS	NH-A	brain
48	chr12:50478800-50480200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:50478800-50480200	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr12:50478800-50480600	Active TSS	Brain Germinal Matrix	brain

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