Variant report

Variant	rs12608852
Chromosome Location	chr19:56859928-56859929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:96)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:96 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:56859780-56859930	HCPEpiC	choroid plexus:	n/a	n/a
2	CTCF	chr19:56859820-56859970	WI-38	lung:	n/a	n/a
3	CTCF	chr19:56859780-56859930	GM12870	blood:	n/a	n/a
4	HDAC2	chr19:56859638-56860007	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr19:56859800-56859950	HEEpiC	esophagus:	n/a	n/a
6	CTCF	chr19:56859780-56859930	WI-38	lung:	n/a	n/a
7	CTCF	chr19:56859780-56859930	HCM	heart:	n/a	n/a
8	CTCF	chr19:56859673-56859933	A549	lung:	n/a	n/a
9	CTCF	chr19:56859780-56859930	GM12866	blood:	n/a	n/a
10	CTCF	chr19:56859820-56859970	HUVEC	blood vessel:	n/a	n/a
11	ARID3A	chr19:56859692-56859938	K562	blood:	n/a	n/a
12	CTCF	chr19:56859686-56860090	MCF-7	breast:	n/a	n/a
13	CTCF	chr19:56859745-56859943	MCF-7	breast:	n/a	n/a
14	ZNF143	chr19:56859672-56860010	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr19:56859779-56859940	Fibrobl	skin:	n/a	n/a
16	FOXA1	chr19:56859593-56860006	HepG2	liver:	n/a	n/a
17	CTCF	chr19:56859780-56859930	GM12864	blood:	n/a	n/a
18	CTCF	chr19:56859693-56859959	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr19:56859820-56859970	NHEK	skin:	n/a	n/a
20	CTCF	chr19:56859687-56859972	HepG2	liver:	n/a	n/a
21	CTCF	chr19:56859800-56859950	HMEC	breast:	n/a	n/a
22	CTCF	chr19:56859800-56859950	SAEC	small airway:	n/a	n/a
23	CTCF	chr19:56859570-56859950	A549	lung:	n/a	n/a
24	CTCF	chr19:56859820-56859970	BJ	skin:	n/a	n/a
25	CTCF	chr19:56859820-56859970	K562	blood:	n/a	n/a
26	CTCF	chr19:56859780-56859930	MCF-7	breast:	n/a	n/a
27	RAD21	chr19:56859651-56860021	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr19:56859800-56859950	HRPEpiC	eye:	n/a	n/a
29	CTCF	chr19:56859780-56859930	HCFaa	heart:	n/a	n/a
30	CTCF	chr19:56859780-56859930	HEEpiC	esophagus:	n/a	n/a
31	MAFF	chr19:56859777-56859977	K562	blood:	n/a	n/a
32	CTCF	chr19:56859820-56859970	HepG2	liver:	n/a	n/a
33	CTCF	chr19:56859780-56859930	WERI-Rb-1	eye:	n/a	n/a
34	CTCF	chr19:56859780-56859930	HRPEpiC	eye:	n/a	n/a
35	CTCF	chr19:56859780-56859930	GM12875	blood:	n/a	n/a
36	CTCF	chr19:56859640-56860012	K562	blood:	n/a	n/a
37	CTCF	chr19:56859780-56859930	GM06990	blood:	n/a	n/a
38	RCOR1	chr19:56858520-56860055	K562	blood:	n/a	n/a
39	CTCF	chr19:56859772-56859974	IMR90	lung:	n/a	n/a
40	CBX3	chr19:56859647-56860104	K562	blood:	n/a	n/a
41	FOXA2	chr19:56859647-56860005	A549	lung:	n/a	n/a
42	CTCF	chr19:56859820-56859970	GM12864	blood:	n/a	n/a
43	RCOR1	chr19:56859733-56860027	K562	blood:	n/a	n/a
44	CTCF	chr19:56859820-56859970	GM12872	blood:	n/a	n/a
45	CTCF	chr19:56859710-56859953	Gliobla	brain:	n/a	n/a
46	FOXA2	chr19:56859694-56859976	HepG2	liver:	n/a	n/a
47	CTCF	chr19:56859780-56859930	GM12867	blood:	n/a	n/a
48	CTCF	chr19:56859780-56859930	GM12872	blood:	n/a	n/a
49	ZNF143	chr19:56859801-56860001	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr19:56859780-56859930	HBMEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56825650..56827475-chr19:56859296..56861906,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267429	TF binding region
ENSG00000131848	Chromatin interaction
ENSG00000267549	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12608516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12610246	0.88[AMR][1000 genomes]
rs12971469	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12976015	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12978701	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12982404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12983342	0.87[AMR][1000 genomes]
rs12983411	1.00[AMR][1000 genomes]
rs2304126	0.88[AMR][1000 genomes]
rs35204149	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4462708	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	esv1837760	chr19:56850795-56877187	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv580357	chr19:56850949-56869794	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv580358	chr19:56851001-56869794	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1829664	chr19:56859584-56864832	ZNF genes & repeats Enhancers Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv442475	chr19:56859584-56864832	Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56854200-56863200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr19:56855000-56870200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr19:56859200-56860000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr19:56859400-56860000	Enhancers	K562	blood
5	chr19:56859400-56872800	Weak transcription	Ovary	ovary
6	chr19:56859600-56862400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:56859600-56862400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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