Variant report

Variant	rs8108440
Chromosome Location	chr19:38888712-38888713
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38888582-38888815	K562	blood:	n/a	n/a
2	POLR2A	chr19:38888573-38888816	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr19:38886771-38892156	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr19:38887810-38888921	U87	brain:	n/a	n/a
5	POLR2A	chr19:38888072-38888879	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr19:38888070-38888832	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr19:38887500-38888949	U87	brain:	n/a	n/a
8	POLR2A	chr19:38887269-38890585	U87	brain:	n/a	n/a
9	POLR2A	chr19:38887005-38894478	MCF10A-Er-Src	breast:	n/a	n/a
10	PBX3	chr19:38888335-38889021	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr19:38887810-38888860	U87	brain:	n/a	n/a
12	POLR2A	chr19:38888012-38888855	HUVEC	blood vessel:	n/a	n/a
13	STAT3	chr19:38888641-38888754	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr19:38886848-38892855	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr19:38888365-38888737	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr19:38887544-38888856	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr19:38888618-38888840	ProgFib	skin:	n/a	n/a
18	POLR2A	chr19:38887402-38891489	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr19:38887776-38888967	HUVEC	blood vessel:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38865462..38867810-chr19:38887445..38890114,2	K562	blood:
2	chr19:38865210..38867100-chr19:38887808..38889837,2	MCF-7	breast:
3	chr19:38886501..38890187-chr19:38891290..38894154,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267473	TF binding region
ENSG00000099341	Chromatin interaction
ENSG00000130244	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10993	1.00[CEU][hapmap]
rs11083454	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11538289	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880301	1.00[CEU][hapmap]
rs2074981	0.81[TSI][hapmap]
rs2302228	1.00[EUR][1000 genomes]
rs3745955	0.80[EUR][1000 genomes]
rs3745963	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3760884	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3786874	0.81[TSI][hapmap]
rs57753437	0.93[EUR][1000 genomes]
rs59491640	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60780508	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6508791	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6508792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6508793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246191	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248540	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257976	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043029	0.81[EUR][1000 genomes]
rs73043030	0.93[EUR][1000 genomes]
rs73043033	0.93[EUR][1000 genomes]
rs73043098	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73044905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044908	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044923	0.80[EUR][1000 genomes]
rs73044926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044930	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044932	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109713	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8112499	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv911661	chr19:38872335-38894829	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv911662	chr19:38872634-38895809	Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38880800-38889200	Weak transcription	Brain Angular Gyrus	brain
2	chr19:38881000-38893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr19:38881000-38893200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr19:38881000-38893200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr19:38881000-38893200	Weak transcription	HSMMtube	muscle
6	chr19:38883600-38891600	Weak transcription	HUVEC	blood vessel
7	chr19:38883600-38893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:38884000-38891600	Weak transcription	A549	lung
9	chr19:38884800-38893200	Weak transcription	NH-A	brain
10	chr19:38885200-38893200	Weak transcription	HSMM	muscle
11	chr19:38885800-38893200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr19:38887000-38893200	Weak transcription	NHDF-Ad	bronchial
13	chr19:38887200-38890800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:38887200-38892400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:38887200-38892400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr19:38887400-38893200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:38887400-38893200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:38887400-38893200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr19:38887400-38893200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:38887400-38893200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr19:38887400-38893200	Weak transcription	NHEK	skin
22	chr19:38887600-38893200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:38887600-38893200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr19:38887600-38893200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:38887600-38893200	Weak transcription	NHLF	lung
26	chr19:38887800-38888800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:38887800-38890200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:38887800-38893200	Weak transcription	Osteobl	bone
29	chr19:38888000-38893200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:38888000-38893200	Weak transcription	Right Atrium	heart
31	chr19:38888400-38890800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:38888400-38891000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:38888600-38888800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell

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