Variant report

Variant	rs58609636
Chromosome Location	chr10:43905483-43905484
allele	C/T
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	chr10:43901067-43905573	HL-60	blood:	n/a	n/a
2	POLR2A	chr10:43901131-43905953	HepG2	liver:	n/a	n/a
3	POLR2A	chr10:43905211-43905553	H1-hESC	embryonic stem cell:	n/a	n/a
4	SMARCB1	chr10:43902578-43905702	Hela-S3	cervix:	n/a	n/a
5	SETDB1	chr10:43903129-43905501	K562	blood:	n/a	chr10:43904422-43904446
6	POLR2A	chr10:43904104-43905590	MCF-7	breast:	n/a	n/a
7	POLR2A	chr10:43902517-43905565	GM12891	blood:	n/a	n/a
8	SIN3AK20	chr10:43902854-43905693	HCT-116	colon:	n/a	n/a
9	POLR2A	chr10:43900942-43905753	GM12878	blood:	n/a	n/a
10	MAX	chr10:43902831-43905956	HCT-116	colon:	n/a	chr10:43904307-43904316 chr10:43903332-43903343 chr10:43903333-43903342 chr10:43904402-43904411 chr10:43903767-43903774
11	POLR2A	chr10:43902392-43905656	GM12892	blood:	n/a	n/a
12	POLR2A	chr10:43900620-43906464	MCF10A-Er-Src	breast:	n/a	n/a
13	RCOR1	chr10:43904177-43905520	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr10:43904126-43905648	HepG2	liver:	n/a	n/a
15	POLR2A	chr10:43900975-43906126	PANC-1	pancreas:	n/a	n/a
16	GTF2F1	chr10:43905358-43905793	Hela-S3	cervix:	n/a	n/a
17	BRCA1	chr10:43904196-43905618	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr10:43902550-43905532	GM18526	blood:	n/a	n/a
19	POLR2A	chr10:43901128-43906303	GM12891	blood:	n/a	n/a
20	POLR2A	chr10:43901152-43906023	GM12878	blood:	n/a	n/a
21	POLR2A	chr10:43901249-43906054	K562	blood:	n/a	n/a
22	POLR2A	chr10:43900693-43905774	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr10:43902308-43905775	PBDE	blood:	n/a	n/a
24	NFYB	chr10:43905227-43905500	GM12878	blood:	n/a	n/a
25	POLR2A	chr10:43900254-43905917	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr10:43902809-43905630	GM12878	blood:	n/a	n/a
27	POLR2A	chr10:43902485-43905609	MCF-7	breast:	n/a	n/a
28	POLR2A	chr10:43902356-43905835	GM12892	blood:	n/a	n/a
29	POLR2A	chr10:43901206-43905768	Hela-S3	cervix:	n/a	n/a
30	E2F4	chr10:43904109-43905732	MCF10A-Er-Src	breast:	n/a	chr10:43904863-43904870 chr10:43904932-43904949 chr10:43904863-43904870 chr10:43904863-43904870 chr10:43904730-43904745 chr10:43904670-43904679
31	POLR2A	chr10:43904069-43905527	HUVEC	blood vessel:	n/a	n/a
32	RFX5	chr10:43904135-43905661	Hela-S3	cervix:	n/a	chr10:43904302-43904317 chr10:43904302-43904317 chr10:43904302-43904317 chr10:43904302-43904315
33	TAF1	chr10:43905229-43905655	GM12878	blood:	n/a	n/a
34	CREB1	chr10:43905043-43905548	A549	lung:	n/a	n/a
35	POLR2A	chr10:43902473-43905624	GM18951	blood:	n/a	n/a
36	PML	chr10:43903985-43905668	GM12878	blood:	n/a	n/a
37	TBP	chr10:43905355-43905687	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr10:43902447-43905993	MCF-7	breast:	n/a	n/a
39	POLR2A	chr10:43902570-43905531	ProgFib	skin:	n/a	n/a
40	POLR2A	chr10:43901229-43906411	Hela-S3	cervix:	n/a	n/a
41	TCF7L2	chr10:43904935-43905659	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr10:43902425-43905654	K562	blood:	n/a	n/a
43	POLR2A	chr10:43902490-43905961	GM12878	blood:	n/a	n/a
44	CHD2	chr10:43902575-43905583	Hela-S3	cervix:	n/a	chr10:43904759-43904769
45	POU2F2	chr10:43904035-43905687	GM12878	blood:	n/a	chr10:43904758-43904770 chr10:43904089-43904101
46	POLR2A	chr10:43902685-43905926	GM12878	blood:	n/a	n/a
47	ZNF384	chr10:43905228-43905750	GM12878	blood:	n/a	n/a
48	CTCF	chr10:43905400-43905550	GM06990	blood:	n/a	n/a
49	BHLHE40	chr10:43905448-43905648	GM12878	blood:	n/a	n/a
50	POLR2A	chr10:43902514-43905678	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:43867647..43875264-chr10:43900659..43906151,11	MCF-7	breast:
2	chr10:43901370..43906375-chr10:43928042..43934083,16	MCF-7	breast:
3	chr10:43904622..43905510-chr18:30050330..30050885,2	Hela-S3	cervix:
4	chr10:43901784..43908257-chr10:43928243..43934263,17	MCF-7	breast:
5	chr10:43899870..43905980-chr10:43953401..43957689,7	MCF-7	breast:
6	chr10:43904675..43905601-chr2:85133815..85134604,2	Hela-S3	cervix:
7	chr10:43887055..43906178-chr10:43946385..43955803,85	K562	blood:
8	chr1:156307804..156308468-chr10:43904566..43905506,2	Hela-S3	cervix:

Variant related genes	Relation type
HNRNPF	TF binding region
ENSG00000163468	Chromatin interaction
ENSG00000186854	Chromatin interaction
ENSG00000252532	Chromatin interaction
ENSG00000141441	Chromatin interaction
ENSG00000150201	Chromatin interaction
ENSG00000163467	Chromatin interaction
ENSG00000243660	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs28788597	1.00[AMR][1000 genomes]
rs57169447	1.00[AMR][1000 genomes]
rs58340819	1.00[AMR][1000 genomes]
rs58594005	1.00[AMR][1000 genomes]
rs60743321	1.00[AMR][1000 genomes]
rs74135709	1.00[AMR][1000 genomes]
rs74135712	1.00[AMR][1000 genomes]
rs74135713	1.00[AMR][1000 genomes]
rs74135718	1.00[AMR][1000 genomes]
rs74135728	1.00[AMR][1000 genomes]
rs74135737	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7915588	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv825355	chr10:43890579-43923802	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv825356	chr10:43893080-43946515	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
8	esv3395522	chr10:43903571-43906119	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43900800-43905600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr10:43901000-43905800	Active TSS	HSMM	muscle
3	chr10:43901200-43905800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr10:43901400-43905600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:43901400-43905800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr10:43901600-43905600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr10:43901600-43905600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr10:43901600-43905600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr10:43901600-43905600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr10:43901600-43905600	Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr10:43901600-43905600	Active TSS	Right Atrium	heart
12	chr10:43901600-43905600	Active TSS	GM12878-XiMat	blood
13	chr10:43901600-43905600	Active TSS	HSMMtube	muscle
14	chr10:43901600-43905600	Active TSS	NHDF-Ad	bronchial
15	chr10:43901600-43905600	Active TSS	NHLF	lung
16	chr10:43901600-43905800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr10:43901600-43905800	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr10:43901600-43906000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:43901800-43905600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:43901800-43905600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr10:43901800-43905600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr10:43901800-43905800	Active TSS	H9 Cell Line	embryonic stem cell
23	chr10:43901800-43905800	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr10:43901800-43905800	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr10:43901800-43905800	Active TSS	Fetal Kidney	kidney
26	chr10:43901800-43906000	Active TSS	Duodenum Mucosa	Duodenum
27	chr10:43902000-43905600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:43902000-43905600	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr10:43902000-43905600	Active TSS	A549	lung
30	chr10:43902000-43905600	Active TSS	Osteobl	bone
31	chr10:43902000-43905800	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr10:43902000-43905800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr10:43902000-43905800	Active TSS	Psoas Muscle	Psoas
34	chr10:43902000-43906000	Active TSS	Muscle Satellite Cultured Cells	--
35	chr10:43902200-43905600	Active TSS	Aorta	Aorta
36	chr10:43902200-43905600	Active TSS	Brain Substantia Nigra	brain
37	chr10:43902200-43905600	Active TSS	Left Ventricle	heart
38	chr10:43902200-43905800	Active TSS	Brain Angular Gyrus	brain
39	chr10:43902400-43905600	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr10:43902400-43905800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr10:43902400-43905800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr10:43902400-43905800	Active TSS	Colonic Mucosa	Colon
43	chr10:43902400-43905800	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr10:43902400-43905800	Active TSS	Rectal Smooth Muscle	rectum
45	chr10:43902600-43906200	Active TSS	Brain Cingulate Gyrus	brain
46	chr10:43902800-43905600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr10:43903200-43906000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr10:43903800-43905600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr10:43903800-43905600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr10:43903800-43905600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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