Variant report

Variant	rs58278424
Chromosome Location	chr19:39684769-39684770
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr19:39684201-39685123	A549	lung:	n/a	n/a
2	SP1	chr19:39684288-39685106	A549	lung:	n/a	n/a
3	CREB1	chr19:39684356-39684966	A549	lung:	n/a	n/a
4	BCL3	chr19:39684339-39685037	A549	lung:	n/a	chr19:39684802-39684815
5	CREB1	chr19:39684482-39684771	A549	lung:	n/a	n/a
6	SIN3AK20	chr19:39684478-39685041	A549	lung:	n/a	n/a
7	FOXA1	chr19:39684761-39685026	HepG2	liver:	n/a	n/a
8	EP300	chr19:39684268-39685123	A549	lung:	n/a	chr19:39684529-39684542
9	REST	chr19:39684333-39685034	A549	lung:	n/a	n/a
10	SIN3AK20	chr19:39684411-39685008	A549	lung:	n/a	n/a
11	FOXA2	chr19:39684731-39684967	HepG2	liver:	n/a	n/a
12	NR3C1	chr19:39684408-39684796	A549	lung:	n/a	n/a
13	FOSL2	chr19:39684329-39684892	A549	lung:	n/a	chr19:39684576-39684584 chr19:39684786-39684800
14	ETS1	chr19:39684428-39685000	A549	lung:	n/a	n/a
15	NR3C1	chr19:39684337-39684946	A549	lung:	n/a	n/a
16	MAX	chr19:39684053-39685113	A549	lung:	n/a	n/a
17	NR3C1	chr19:39684265-39684994	A549	lung:	n/a	n/a
18	NR3C1	chr19:39684360-39684844	A549	lung:	n/a	n/a
19	BCL3	chr19:39684408-39685102	A549	lung:	n/a	chr19:39684802-39684815
20	FOXA2	chr19:39684467-39685036	A549	lung:	n/a	n/a
21	TCF12	chr19:39684475-39685056	A549	lung:	n/a	n/a
22	EP300	chr19:39684259-39685048	A549	lung:	n/a	chr19:39684529-39684542
23	SP1	chr19:39684220-39685128	A549	lung:	n/a	n/a
24	NR3C1	chr19:39684302-39684899	A549	lung:	n/a	n/a
25	MYC	chr19:39684461-39684819	MCF-7	breast:	n/a	n/a
26	EBF1	chr19:39684759-39684777	GM12878	blood:	n/a	n/a
27	ELF1	chr19:39684326-39684839	A549	lung:	n/a	n/a
28	FOXA2	chr19:39684355-39685172	A549	lung:	n/a	n/a
29	GATA3	chr19:39684340-39685125	A549	lung:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39677174..39681975-chr19:39683439..39687085,6	MCF-7	breast:
2	chr19:39683585..39686543-chr19:39818875..39821716,2	MCF-7	breast:
3	chr19:39666393..39669331-chr19:39683166..39685486,2	K562	blood:
4	chr19:39521369..39524252-chr19:39683910..39686549,2	MCF-7	breast:
5	chr19:39610539..39613482-chr19:39683239..39685361,3	MCF-7	breast:
6	chr19:39645920..39648679-chr19:39684558..39687537,2	MCF-7	breast:
7	chr19:39615742..39618240-chr19:39683167..39686406,3	MCF-7	breast:
8	chr19:39684528..39687372-chr19:39688107..39690948,3	MCF-7	breast:
9	chr19:39676778..39680967-chr19:39681960..39686095,4	K562	blood:

No data

Variant related genes	Relation type
NCCRP1	TF binding region
ENSG00000130669	Chromatin interaction
ENSG00000161243	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11083511	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083512	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083513	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668945	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672471	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672475	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672479	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462614	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609028	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609203	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12610064	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12610093	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12610618	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974792	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12976040	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808652	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013626	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2319154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319156	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2873914	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58016205	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7508321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104935	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8106521	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs892015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs892016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv1796470	chr19:39679379-39714631	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39657800-39687600	Weak transcription	Right Atrium	heart
2	chr19:39669200-39685800	Weak transcription	NHEK	skin
3	chr19:39678600-39687400	Weak transcription	Spleen	Spleen
4	chr19:39683400-39684800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:39683800-39686600	Weak transcription	HMEC	breast
6	chr19:39684200-39684800	Enhancers	Liver	Liver
7	chr19:39684200-39684800	Enhancers	Esophagus	oesophagus
8	chr19:39684200-39684800	Enhancers	Gastric	stomach
9	chr19:39684200-39684800	Enhancers	Stomach Mucosa	stomach
10	chr19:39684200-39685000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:39684200-39685800	Enhancers	Duodenum Mucosa	Duodenum
12	chr19:39684400-39684800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:39684400-39684800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:39684400-39684800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:39684400-39684800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:39684400-39684800	Flanking Active TSS	Pancreas	Pancrea
17	chr19:39684400-39684800	Flanking Active TSS	HepG2	liver
18	chr19:39684400-39685000	Flanking Active TSS	A549	lung
19	chr19:39684400-39685400	Enhancers	Fetal Intestine Large	intestine
20	chr19:39684400-39685400	Enhancers	Placenta	Placenta
21	chr19:39684400-39686000	Enhancers	Hela-S3	cervix
22	chr19:39684600-39684800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:39684600-39684800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
24	chr19:39684600-39684800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr19:39684600-39684800	Bivalent Enhancer	Fetal Brain Female	brain
26	chr19:39684600-39684800	Enhancers	HSMM	muscle
27	chr19:39684600-39684800	Bivalent Enhancer	NHDF-Ad	bronchial
28	chr19:39684600-39685000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:39684600-39685000	Enhancers	HSMMtube	muscle

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