Variant report

Variant	rs8100659
Chromosome Location	chr19:39685712-39685713
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr19:39685650-39685912	K562	blood:	n/a	n/a
2	RCOR1	chr19:39685582-39685875	K562	blood:	n/a	n/a
3	MXI1	chr19:39685559-39686265	SK-N-SH	brain:	n/a	chr19:39686059-39686074 chr19:39686057-39686072
4	ZNF143	chr19:39685706-39685889	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 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	chr19:39521369..39524252-chr19:39683910..39686549,2	MCF-7	breast:
4	chr19:39645920..39648679-chr19:39684558..39687537,2	MCF-7	breast:
5	chr19:39615742..39618240-chr19:39683167..39686406,3	MCF-7	breast:
6	chr19:39684528..39687372-chr19:39688107..39690948,3	MCF-7	breast:
7	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: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11083511	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083512	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083513	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668945	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672471	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672475	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672479	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462614	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609028	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609203	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12610064	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12610093	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12610618	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974074	0.83[CHB][hapmap]
rs12974792	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12976040	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808652	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013626	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2319154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319156	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2873914	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58016205	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58278424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7508321	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104935	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8106521	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs892015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs892016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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:25 , 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	chr19:39684400-39686000	Enhancers	Hela-S3	cervix
7	chr19:39684800-39685800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:39684800-39685800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr19:39684800-39685800	Weak transcription	Esophagus	oesophagus
10	chr19:39684800-39686000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:39684800-39686400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:39684800-39686600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:39685000-39686400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:39685000-39690000	Enhancers	A549	lung
15	chr19:39685400-39686400	Bivalent Enhancer	Fetal Intestine Large	intestine
16	chr19:39685400-39686400	Bivalent Enhancer	Fetal Intestine Small	intestine
17	chr19:39685400-39687600	Enhancers	Pancreas	Pancrea
18	chr19:39685400-39688800	Bivalent Enhancer	Placenta	Placenta
19	chr19:39685600-39686200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
20	chr19:39685600-39686800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr19:39685600-39686800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
22	chr19:39685600-39688000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:39685600-39688200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
24	chr19:39685600-39688200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
25	chr19:39685600-39688200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood

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