Variant report

Variant	rs563980647
Chromosome Location	chr15:59664405-59664406
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	POLR2A	chr15:59663811-59665404	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr15:59663560-59665444	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:59660865-59666082	Hela-S3	cervix:	n/a	n/a
4	RAD21	chr15:59664204-59665461	IMR90	lung:	n/a	chr15:59664358-59664372 chr15:59664300-59664314
5	POLR2A	chr15:59664363-59665369	GM12878	blood:	n/a	n/a
6	TAF1	chr15:59664317-59665617	A549	lung:	n/a	n/a
7	POLR2A	chr15:59663366-59667532	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr15:59663801-59665365	GM12878	blood:	n/a	n/a
9	ZBTB7A	chr15:59663567-59665447	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr15:59664026-59665715	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr15:59663729-59665390	GM12878	blood:	n/a	chr15:59664162-59664172 chr15:59664349-59664358 chr15:59664440-59664449 chr15:59664104-59664114
12	YY1	chr15:59664282-59665308	GM12878	blood:	n/a	chr15:59665090-59665106 chr15:59664960-59664974 chr15:59664300-59664314 chr15:59664675-59664689 chr15:59664304-59664315
13	POLR2A	chr15:59664172-59665500	H1-hESC	embryonic stem cell:	n/a	n/a
14	TCF3	chr15:59663971-59664844	GM12878	blood:	n/a	chr15:59664187-59664201
15	POLR2A	chr15:59664297-59665444	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:59664399-59665526	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr15:59663574-59665764	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr15:59663873-59665375	Raji	blood:	n/a	n/a
19	SIN3A	chr15:59663611-59665694	H1-hESC	embryonic stem cell:	n/a	chr15:59664197-59664206 chr15:59664008-59664021 chr15:59664211-59664222 chr15:59664152-59664165 chr15:59664185-59664198
20	POLR2A	chr15:59664087-59665519	GM12892	blood:	n/a	n/a
21	POLR2A	chr15:59663987-59665398	GM19099	blood:	n/a	n/a
22	YY1	chr15:59663948-59665264	GM12892	blood:	n/a	chr15:59665090-59665106 chr15:59664221-59664230 chr15:59664219-59664230 chr15:59664194-59664208 chr15:59664122-59664136 chr15:59664071-59664082 chr15:59664960-59664974 chr15:59664160-59664169 chr15:59664300-59664314 chr15:59664103-59664112 chr15:59664127-59664136 chr15:59664675-59664689 chr15:59664101-59664115 chr15:59664304-59664315
23	MAX	chr15:59663604-59665694	HepG2	liver:	n/a	chr15:59664162-59664172 chr15:59664349-59664358 chr15:59664440-59664449 chr15:59664104-59664114
24	POLR2A	chr15:59664326-59665650	U87	brain:	n/a	n/a
25	TCF7L2	chr15:59663932-59665246	HCT-116	colon:	n/a	n/a
26	MXI1	chr15:59663856-59665465	HepG2	liver:	n/a	chr15:59664434-59664449
27	ZNF143	chr15:59664319-59665395	GM12878	blood:	n/a	chr15:59664737-59664755 chr15:59664349-59664367
28	E2F6	chr15:59664377-59665858	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr15:59664282-59665656	U87	brain:	n/a	n/a
30	PML	chr15:59664320-59665832	GM12878	blood:	n/a	n/a
31	STAT5A	chr15:59664380-59665036	GM12878	blood:	n/a	n/a
32	GATA3	chr15:59664361-59665830	A549	lung:	n/a	chr15:59665425-59665434
33	RUNX3	chr15:59664207-59665483	GM12878	blood:	n/a	n/a
34	BHLHE40	chr15:59663764-59665849	GM12878	blood:	n/a	chr15:59664075-59664091 chr15:59664192-59664208 chr15:59664333-59664349 chr15:59664294-59664310
35	POLR2A	chr15:59663849-59664454	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr15:59663964-59665289	GM12878	blood:	n/a	n/a
37	TAF1	chr15:59664305-59665621	ECC-1	luminal epithelium:	n/a	n/a
38	YY1	chr15:59664144-59665459	ECC-1	luminal epithelium:	n/a	chr15:59665090-59665106 chr15:59664221-59664230 chr15:59664219-59664230 chr15:59664194-59664208 chr15:59664960-59664974 chr15:59664160-59664169 chr15:59664300-59664314 chr15:59664675-59664689 chr15:59664304-59664315
39	MAX	chr15:59663598-59665891	ECC-1	luminal epithelium:	n/a	chr15:59664162-59664172 chr15:59664349-59664358 chr15:59664440-59664449 chr15:59664104-59664114
40	YY1	chr15:59664044-59664638	HepG2	liver:	n/a	chr15:59664221-59664230 chr15:59664219-59664230 chr15:59664194-59664208 chr15:59664122-59664136 chr15:59664071-59664082 chr15:59664160-59664169 chr15:59664300-59664314 chr15:59664103-59664112 chr15:59664127-59664136 chr15:59664101-59664115 chr15:59664304-59664315
41	SMC3	chr15:59664359-59664644	GM12878	blood:	n/a	n/a
42	JUND	chr15:59664282-59665527	A549	lung:	n/a	chr15:59664631-59664645 chr15:59664838-59664847
43	POLR2A	chr15:59663669-59665532	GM12878	blood:	n/a	n/a
44	TBP	chr15:59664097-59665640	H1-hESC	embryonic stem cell:	n/a	n/a
45	PBX3	chr15:59664360-59664491	GM12878	blood:	n/a	n/a
46	TCF12	chr15:59664227-59665676	A549	lung:	n/a	chr15:59664430-59664437
47	EGR1	chr15:59664318-59664493	GM12878	blood:	n/a	chr15:59664361-59664375
48	POLR2A	chr15:59664136-59664469	Gliobla	brain:	n/a	n/a
49	HA-E2F1	chr15:59663896-59664929	Hela-S3	cervix:	n/a	chr15:59664098-59664108 chr15:59664127-59664136 chr15:59664163-59664172 chr15:59664219-59664229 chr15:59664221-59664230
50	POLR2A	chr15:59664268-59664466	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45003542..45004263-chr15:59664269..59664993,2	Hela-S3	cervix:
2	chr15:59662898..59664919-chr15:59728478..59730904,2	MCF-7	breast:
3	chr15:59567773..59570497-chr15:59662817..59664503,2	MCF-7	breast:
4	chr15:59518511..59521491-chr15:59664302..59666468,2	MCF-7	breast:
5	chr15:59664310..59665106-chr17:42276644..42277426,2	Hela-S3	cervix:
6	chr15:59664159..59664700-chr5:72251889..72252399,2	Hela-S3	cervix:

Variant related genes	Relation type
FAM81A	TF binding region
ENSG00000087152	Chromatin interaction
ENSG00000157483	Chromatin interaction
ENSG00000157107	Chromatin interaction
ENSG00000166710	Chromatin interaction
ENSG00000157470	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv934082	chr15:59608605-59733211	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv457175	chr15:59609753-59681214	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv569603	chr15:59609753-59681214	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv471246	chr15:59610743-59681214	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv904274	chr15:59623576-59689378	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv904275	chr15:59648633-59726610	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
8	nsv904276	chr15:59648633-59743010	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	n/a
9	esv3342886	chr15:59663285-59665833	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59662000-59666000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:59662200-59665800	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr15:59662600-59665800	Active TSS	NHLF	lung
4	chr15:59662600-59666000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr15:59662600-59666000	Active TSS	Rectal Smooth Muscle	rectum
6	chr15:59662600-59666200	Active TSS	Colonic Mucosa	Colon
7	chr15:59662600-59666600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr15:59662600-59667600	Active TSS	GM12878-XiMat	blood
9	chr15:59662800-59665600	Active TSS	Fetal Intestine Large	intestine
10	chr15:59662800-59665800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:59662800-59665800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:59662800-59665800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr15:59662800-59665800	Active TSS	Left Ventricle	heart
14	chr15:59662800-59666000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:59662800-59666000	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr15:59662800-59666200	Active TSS	Fetal Intestine Small	intestine
17	chr15:59663000-59664600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr15:59663000-59665400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:59663000-59665600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:59663000-59665800	Active TSS	Brain Angular Gyrus	brain
21	chr15:59663000-59665800	Active TSS	Right Atrium	heart
22	chr15:59663000-59665800	Active TSS	HSMMtube	muscle
23	chr15:59663000-59665800	Active TSS	NHDF-Ad	bronchial
24	chr15:59663000-59666000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr15:59663000-59666000	Active TSS	Aorta	Aorta
26	chr15:59663000-59666200	Active TSS	Duodenum Mucosa	Duodenum
27	chr15:59663200-59665600	Active TSS	Psoas Muscle	Psoas
28	chr15:59663200-59665800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:59663200-59665800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:59663200-59665800	Active TSS	Right Ventricle	heart
31	chr15:59663200-59666000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:59663400-59665400	Active TSS	Stomach Mucosa	stomach
33	chr15:59663400-59665600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr15:59663400-59665600	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr15:59663400-59665600	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr15:59663400-59665600	Active TSS	NHEK	skin
37	chr15:59663400-59665800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:59663400-59665800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:59663400-59665800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:59663400-59665800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:59663400-59665800	Active TSS	Brain Cingulate Gyrus	brain
42	chr15:59663400-59665800	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr15:59663400-59665800	Active TSS	Fetal Kidney	kidney
44	chr15:59663400-59665800	Active TSS	HSMM	muscle
45	chr15:59663400-59666000	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr15:59663400-59666000	Active TSS	Ovary	ovary
47	chr15:59663400-59666000	Active TSS	HMEC	breast
48	chr15:59663600-59664600	Bivalent/Poised TSS	Fetal Thymus	thymus
49	chr15:59663600-59665000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
50	chr15:59663600-59665400	Active TSS	Esophagus	oesophagus

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