Variant report

Variant	rs2013626
Chromosome Location	chr19:39685129-39685130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr19:39684355-39685172	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
ENSG00000161243	Chromatin interaction
ENSG00000130669	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	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083512	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083513	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083514	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11668945	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11672471	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11672475	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11672479	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11672787	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12462614	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12609028	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12609203	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12610064	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12610093	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12610618	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12974792	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12976040	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1808652	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2319154	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2319155	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2319156	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2873914	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58016205	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58278424	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7508321	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8100659	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8103222	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8103224	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8104935	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8106521	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs892015	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs892016	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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:17 , 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	chr19:39683800-39686600	Weak transcription	HMEC	breast
5	chr19:39684200-39685800	Enhancers	Duodenum Mucosa	Duodenum
6	chr19:39684400-39685400	Enhancers	Fetal Intestine Large	intestine
7	chr19:39684400-39685400	Enhancers	Placenta	Placenta
8	chr19:39684400-39686000	Enhancers	Hela-S3	cervix
9	chr19:39684800-39685800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:39684800-39685800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:39684800-39685800	Weak transcription	Esophagus	oesophagus
12	chr19:39684800-39686000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:39684800-39686400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:39684800-39686600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:39685000-39685400	Weak transcription	Pancreas	Pancrea
16	chr19:39685000-39686400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:39685000-39690000	Enhancers	A549	lung

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