Variant report

Variant	rs12982404
Chromosome Location	chr19:56862069-56862070
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	CTCF	chr19:56861998-56862087	GM19240	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
2	CTCF	chr19:56862000-56862150	Hela-S3	cervix:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
3	CTCF	chr19:56861940-56862090	HL-60	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
4	RAD21	chr19:56861860-56862194	HCT-116	colon:	n/a	chr19:56862004-56862023 chr19:56862014-56862021
5	CTCF	chr19:56861960-56862110	HMEC	breast:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
6	MAFK	chr19:56861893-56862099	K562	blood:	n/a	chr19:56861941-56861956
7	SIN3AK20	chr19:56861797-56862191	MCF-7	breast:	n/a	n/a
8	RAD21	chr19:56861734-56862246	HCT-116	colon:	n/a	chr19:56862004-56862023 chr19:56862014-56862021
9	ZNF217	chr19:56861861-56862099	MCF-7	breast:	n/a	n/a
10	CTCF	chr19:56861786-56862207	K562	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
11	CTCF	chr19:56861942-56862129	LNCaP	prostate:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
12	CTCF	chr19:56861843-56862173	HUVEC	blood vessel:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
13	RAD21	chr19:56861721-56862205	A549	lung:	n/a	chr19:56862004-56862023 chr19:56862014-56862021
14	CTCF	chr19:56861940-56862090	GM12871	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
15	CTCF	chr19:56861920-56862070	A549	lung:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
16	RAD21	chr19:56861875-56862135	MCF-7	breast:	n/a	chr19:56862004-56862023 chr19:56862014-56862021
17	CTCF	chr19:56861878-56862158	GM12878	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
18	CTCF	chr19:56861938-56862129	NHEK	skin:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
19	CBX3	chr19:56861759-56862199	K562	blood:	n/a	n/a
20	SMC3	chr19:56861827-56862182	GM12878	blood:	n/a	chr19:56862008-56862022
21	CTCF	chr19:56861816-56862215	K562	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
22	STAT3	chr19:56861985-56862169	GM12878	blood:	n/a	n/a
23	CTCF	chr19:56861960-56862110	K562	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
24	CTCF	chr19:56861940-56862090	NHDF-neo	bronchial:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
25	CTCF	chr19:56861920-56862070	SK-N-SH_RA	brain:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
26	CTCF	chr19:56861960-56862110	HRPEpiC	eye:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
27	CTCF	chr19:56861960-56862110	HepG2	liver:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
28	CTCF	chr19:56862011-56862083	GM19238	blood:	n/a	n/a
29	CTCF	chr19:56861940-56862090	GM12870	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
30	CTCF	chr19:56861940-56862090	AG04450	lung:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
31	SMC3	chr19:56861862-56862190	HepG2	liver:	n/a	chr19:56862008-56862022
32	CTCF	chr19:56861652-56862411	SK-N-SH	brain:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
33	CTCF	chr19:56861886-56862171	Lung_OC	lung:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
34	CTCF	chr19:56861841-56862167	Spleen_OC	spleen:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
35	CTCF	chr19:56861973-56862071	MCF-7	breast:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
36	CTCF	chr19:56861960-56862110	GM12874	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
37	CTCF	chr19:56861940-56862090	AG04449	skin:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
38	CTCF	chr19:56861866-56862155	SK-N-SH_RA	brain:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
39	CTCF	chr19:56861920-56862070	HUVEC	blood vessel:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
40	CTCF	chr19:56861881-56862157	Pancreas_OC	pancreas:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
41	CTCF	chr19:56861920-56862070	GM12874	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
42	EP300	chr19:56861821-56862129	K562	blood:	n/a	n/a
43	CTCF	chr19:56861940-56862090	GM12873	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
44	CTCF	chr19:56861920-56862070	AG04450	lung:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
45	CTCF	chr19:56861821-56862171	MCF-7	breast:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
46	ATF1	chr19:56861870-56862141	K562	blood:	n/a	n/a
47	CTCF	chr19:56861940-56862090	SAEC	small airway:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
48	RAD21	chr19:56861797-56862139	MCF-7	breast:	n/a	chr19:56862004-56862023 chr19:56862014-56862021
49	RAD21	chr19:56861892-56862089	A549	lung:	n/a	chr19:56862004-56862023 chr19:56862014-56862021
50	CTCF	chr19:56861940-56862090	GM12864	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023

No.	Distal block	Cell Line	Cell type
1	chr19:56861231..56863974-chr19:56864374..56866865,3	K562	blood:
2	chr19:56821112..56821613-chr19:56861782..56862434,2	K562	blood:
3	chr19:56861231..56864651-chr19:56864910..56868187,3	K562	blood:

Variant related genes	Relation type
ENSG00000267429	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10419074	0.82[CEU][hapmap]
rs12608516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12608852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610246	0.82[CEU][hapmap];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]
rs12983342	0.82[CEU][hapmap];0.87[AMR][1000 genomes]
rs12983411	1.00[AMR][1000 genomes]
rs2304126	0.82[CEU][hapmap];0.88[AMR][1000 genomes]
rs35204149	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4462708	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8107120	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	nsv828648	chr19:56861685-56864862	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	4 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	chr19:56859400-56872800	Weak transcription	Ovary	ovary
4	chr19:56859600-56862400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:56859600-56862400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:56860000-56862800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:56862000-56868400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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