Variant report

Variant	rs562464564
Chromosome Location	chr10:116581399-116581400
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	chr10:116581212-116581785	K562	blood:	n/a	n/a
2	RFX5	chr10:116580617-116581604	Hela-S3	cervix:	n/a	n/a
3	TAF1	chr10:116581372-116581731	HepG2	liver:	n/a	n/a
4	CTCF	chr10:116581289-116581732	MCF-7	breast:	n/a	chr10:116581357-116581370 chr10:116581354-116581372
5	TAF1	chr10:116581371-116581558	PFSK-1	brain:	n/a	n/a
6	CTCF	chr10:116581265-116581656	Gliobla	brain:	n/a	chr10:116581357-116581370 chr10:116581354-116581372
7	RAD21	chr10:116581188-116581585	HepG2	liver:	n/a	chr10:116581360-116581372 chr10:116581355-116581374
8	UBTF	chr10:116581327-116582529	K562	blood:	n/a	n/a
9	CTCF	chr10:116581262-116581688	GM12891	blood:	n/a	chr10:116581357-116581370 chr10:116581354-116581372
10	SMC3	chr10:116581213-116581672	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr10:116581178-116582104	HUVEC	blood vessel:	n/a	n/a
12	CTCF	chr10:116581214-116581559	K562	blood:	n/a	chr10:116581357-116581370 chr10:116581354-116581372
13	POLR2A	chr10:116581072-116581787	GM12891	blood:	n/a	n/a
14	CTCF	chr10:116581320-116581470	HMF	breast:	n/a	chr10:116581357-116581370 chr10:116581354-116581372
15	JUND	chr10:116581209-116581574	K562	blood:	n/a	n/a
16	MAX	chr10:116581105-116581911	GM12878	blood:	n/a	n/a
17	EBF1	chr10:116581268-116581428	GM12878	blood:	n/a	n/a
18	POLR2A	chr10:116581348-116582052	Raji	blood:	n/a	n/a
19	RAD21	chr10:116581270-116581593	A549	lung:	n/a	chr10:116581360-116581372 chr10:116581355-116581374
20	CHD2	chr10:116581215-116581806	Hela-S3	cervix:	n/a	chr10:116581716-116581726
21	POLR2A	chr10:116581195-116581729	Hela-S3	cervix:	n/a	n/a
22	EGR1	chr10:116581223-116581563	K562	blood:	n/a	chr10:116581423-116581437
23	CTCF	chr10:116581276-116581642	GM10248	blood:	n/a	chr10:116581357-116581370 chr10:116581354-116581372
24	POLR2A	chr10:116581280-116581992	A549	lung:	n/a	n/a
25	CTCF	chr10:116581331-116581633	Lung_OC	lung:	n/a	chr10:116581357-116581370 chr10:116581354-116581372
26	CTCF	chr10:116581317-116581649	Pancreas_OC	pancreas:	n/a	chr10:116581357-116581370 chr10:116581354-116581372
27	YY1	chr10:116581364-116581610	K562	blood:	n/a	n/a
28	CTCF	chr10:116581380-116581530	HAc	cerebellar:	n/a	n/a
29	POLR2A	chr10:116581009-116582855	HUVEC	blood vessel:	n/a	n/a
30	EGR1	chr10:116581167-116581622	ECC-1	luminal epithelium:	n/a	chr10:116581423-116581437
31	ZBTB7A	chr10:116581310-116581506	HepG2	liver:	n/a	n/a
32	PAX5	chr10:116581222-116581730	GM12892	blood:	n/a	n/a
33	POLR2A	chr10:116581313-116581622	U87	brain:	n/a	n/a
34	E2F6	chr10:116581267-116581549	K562	blood:	n/a	n/a
35	EP300	chr10:116581268-116581650	GM12878	blood:	n/a	chr10:116581569-116581578
36	MXI1	chr10:116580831-116581578	Hela-S3	cervix:	n/a	n/a
37	TAF1	chr10:116581191-116582392	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr10:116581290-116581932	HepG2	liver:	n/a	n/a
39	BACH1	chr10:116581091-116581507	H1-hESC	embryonic stem cell:	n/a	n/a
40	RAD21	chr10:116581277-116581571	K562	blood:	n/a	chr10:116581360-116581372 chr10:116581355-116581374
41	USF1	chr10:116581133-116581535	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr10:116581164-116582526	GM18526	blood:	n/a	n/a
43	YY1	chr10:116581161-116582138	GM12892	blood:	n/a	chr10:116581770-116581779 chr10:116581771-116581782 chr10:116581749-116581763 chr10:116581752-116581763 chr10:116581922-116581931 chr10:116581773-116581782 chr10:116581972-116581986
44	CTCF	chr10:116581320-116581470	HCM	heart:	n/a	chr10:116581357-116581370 chr10:116581354-116581372
45	CTCF	chr10:116581023-116581632	HCT-116	colon:	n/a	chr10:116581357-116581370 chr10:116581354-116581372 chr10:116581103-116581111
46	YY1	chr10:116581294-116581688	K562	blood:	n/a	n/a
47	ELF1	chr10:116581235-116581896	GM12878	blood:	n/a	chr10:116581773-116581782 chr10:116581765-116581777 chr10:116581771-116581783 chr10:116581770-116581779
48	TCF12	chr10:116581141-116582004	ECC-1	luminal epithelium:	n/a	chr10:116581154-116581163
49	YY1	chr10:116581211-116581634	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr10:116581216-116581683	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:116581358-116581408	PFSK-1	brain:	n/a
2	chr10:116581358-116581408	ECC-1	luminal epithelium:	n/a
3	chr10:116581358-116581408	ovcar-3	ovarian:	n/a
4	chr10:116581358-116581408	HEK293	kidney:	embryo
5	chr10:116581358-116581408	PrEC	prostate:	n/a
6	chr10:116581358-116581408	GM19239	blood:	n/a
7	chr10:116581358-116581408	SKMC	muscle:	n/a
8	chr10:116581358-116581408	Caco-2	colon:	n/a
9	chr10:116581358-116581408	HCT-116	colon:	n/a
10	chr10:116581358-116581408	MCF-7	breast:	n/a
11	chr10:116581358-116581408	GM06990	blood:	n/a
12	chr10:116581358-116581408	BE2_C	brain:	n/a
13	chr10:116581358-116581408	GM12891	blood:	n/a
14	chr10:116581358-116581408	HCF	heart:	n/a
15	chr10:116581358-116581408	HUVEC	blood vessel:	n/a
16	chr10:116581358-116581408	HNPCEpiC	eye:	n/a
17	chr10:116581358-116581408	K562	blood:	n/a
18	chr10:116581358-116581408	AG10803	skin:	n/a
19	chr10:116581358-116581408	LNCaP	prostate:	n/a
20	chr10:116581358-116581408	HepG2	liver:	n/a
21	chr10:116581358-116581408	HRPEpiC	eye:	n/a
22	chr10:116581358-116581408	SK-N-MC	brain:	n/a
23	chr10:116581358-116581408	AG04450	lung:	fetal
24	chr10:116581358-116581408	HIPEpiC	eye:	n/a
25	chr10:116581358-116581408	U87	brain:	n/a
26	chr10:116581358-116581408	HRCEpiC	kidney:	n/a
27	chr10:116581358-116581408	RPTEC	kidney:	n/a
28	chr10:116581358-116581408	HEEpiC	esophagus:	n/a
29	chr10:116581358-116581408	BJ	skin:	n/a
30	chr10:116581358-116581408	Jurkat	blood:	n/a
31	chr10:116581358-116581408	NHDF-neo	bronchial:	n/a
32	chr10:116581358-116581408	A549	lung:	n/a
33	chr10:116581358-116581408	HCM	heart:	n/a
34	chr10:116581358-116581408	HPAEpiC	pulmonary alveolar:	n/a
35	chr10:116581358-116581408	PANC-1	pancreas:	n/a
36	chr10:116581358-116581408	HCPEpiC	choroid plexus:	n/a
37	chr10:116581358-116581408	NHBE	bronchial:	n/a
38	chr10:116581358-116581408	MCF10A-Er-Src	breast:	n/a
39	chr10:116581358-116581408	SAEC	small airway:	n/a
40	chr10:116581358-116581408	GM12892	blood:	n/a
41	chr10:116581358-116581408	Hepatocyte	liver:	n/a
42	chr10:116581358-116581408	Hela-S3	cervix:	n/a
43	chr10:116581358-116581408	IMR90	lung:	fetal
44	chr10:116581358-116581408	CMK	blood:	n/a
45	chr10:116581358-116581408	HL-60	blood:	n/a
46	chr10:116581358-116581408	SK-N-SH	brain:	n/a
47	chr10:116581358-116581408	ProgFib	skin:	n/a
48	chr10:116581358-116581408	GM12878	blood:	n/a
49	chr10:116581358-116581408	NB4	blood:	n/a
50	chr10:116581358-116581408	H1-hESC	embryonic stem cell:	embryo

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116580811..116581705-chr8:27631902..27632494,2	Hela-S3	cervix:
2	chr10:116567584..116574580-chr10:116575101..116583231,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABLIM1-1	chr10:116581032-116581425	NONHSAT016464

Variant related genes	Relation type
FAM160B1	TF binding region
FAM160B1	CpG island
ENSG00000171320	Chromatin interaction
ENSG00000215760	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	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	esv1814163	chr10:116519705-116582581	Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv518081	chr10:116576189-116582502	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv3338822	chr10:116579462-116583960	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3407216	chr10:116580587-116583135	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv3343755	chr10:116580762-116583210	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116579400-116583600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr10:116579800-116583600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr10:116580200-116582200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr10:116580600-116581400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr10:116580600-116581400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr10:116580600-116581400	Flanking Active TSS	Dnd41	blood
7	chr10:116580600-116581400	Flanking Active TSS	HUVEC	blood vessel
8	chr10:116580600-116581600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr10:116580600-116582800	Active TSS	NHEK	skin
10	chr10:116580600-116583000	Active TSS	Placenta Amnion	Placenta Amnion
11	chr10:116580600-116583600	Active TSS	GM12878-XiMat	blood
12	chr10:116580600-116583800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr10:116580600-116584600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:116580800-116581400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr10:116580800-116582800	Active TSS	Hela-S3	cervix
16	chr10:116580800-116583000	Active TSS	Brain Angular Gyrus	brain
17	chr10:116580800-116583200	Active TSS	A549	lung
18	chr10:116580800-116583400	Active TSS	NH-A	brain
19	chr10:116580800-116584200	Active TSS	NHLF	lung
20	chr10:116580800-116584600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr10:116581000-116581400	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr10:116581000-116581400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr10:116581000-116581400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr10:116581000-116581400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr10:116581000-116581400	Active TSS	Fetal Brain Male	brain
26	chr10:116581000-116581400	Flanking Active TSS	HMEC	breast
27	chr10:116581000-116581600	Active TSS	Brain Germinal Matrix	brain
28	chr10:116581000-116581800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:116581000-116582200	Active TSS	Primary T cells fromperipheralblood	blood
30	chr10:116581000-116582400	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr10:116581000-116582400	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr10:116581000-116582400	Active TSS	HepG2	liver
33	chr10:116581000-116582600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr10:116581000-116582600	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr10:116581000-116582600	Active TSS	Primary T cells from cord blood	blood
36	chr10:116581000-116582600	Active TSS	Brain Anterior Caudate	brain
37	chr10:116581000-116582800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr10:116581000-116582800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr10:116581000-116582800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr10:116581000-116582800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr10:116581000-116582800	Active TSS	Fetal Brain Female	brain
42	chr10:116581000-116582800	Active TSS	Fetal Kidney	kidney
43	chr10:116581000-116583000	Active TSS	H1 Cell Line	embryonic stem cell
44	chr10:116581000-116583000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr10:116581000-116583000	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr10:116581000-116583000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr10:116581000-116583000	Active TSS	Brain Cingulate Gyrus	brain
48	chr10:116581000-116583000	Active TSS	Brain Hippocampus Middle	brain
49	chr10:116581000-116583000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr10:116581000-116583000	Active TSS	Brain Substantia Nigra	brain

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