Variant report

Variant	rs73044926
Chromosome Location	chr19:38887463-38887464
allele	C/T
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	POLR2A	chr19:38886771-38892156	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr19:38887269-38890585	U87	brain:	n/a	n/a
3	POLR2A	chr19:38887005-38894478	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr19:38886848-38892855	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr19:38887449-38887739	U87	brain:	n/a	n/a
6	POLR2A	chr19:38886934-38887517	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr19:38887402-38891489	SK-N-SH	brain:	n/a	n/a

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

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

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11083454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11538289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2302228	1.00[EUR][1000 genomes]
rs3745955	0.80[EUR][1000 genomes]
rs3745963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3760884	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257976	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]
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]
rs8108440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8112499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	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
12	esv3425239	chr19:38885137-38887985	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38880200-38887600	Weak transcription	Right Atrium	heart
2	chr19:38880800-38889200	Weak transcription	Brain Angular Gyrus	brain
3	chr19:38881000-38887600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:38881000-38893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:38881000-38893200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr19:38881000-38893200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr19:38881000-38893200	Weak transcription	HSMMtube	muscle
8	chr19:38882600-38888000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:38883000-38888000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:38883200-38887800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:38883600-38891600	Weak transcription	HUVEC	blood vessel
12	chr19:38883600-38893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:38883800-38887600	Strong transcription	NHLF	lung
14	chr19:38883800-38887800	Strong transcription	Osteobl	bone
15	chr19:38883800-38888400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:38884000-38891600	Weak transcription	A549	lung
17	chr19:38884800-38893200	Weak transcription	NH-A	brain
18	chr19:38885200-38893200	Weak transcription	HSMM	muscle
19	chr19:38885800-38893200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:38886200-38887600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:38886200-38888200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:38886400-38887600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:38886600-38887800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:38887000-38887600	Enhancers	Primary T cells fromperipheralblood	blood
25	chr19:38887000-38887600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:38887000-38887600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:38887000-38893200	Weak transcription	NHDF-Ad	bronchial
28	chr19:38887200-38887600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr19:38887200-38888000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:38887200-38890800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:38887200-38892400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:38887200-38892400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr19:38887400-38893200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:38887400-38893200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr19:38887400-38893200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr19:38887400-38893200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr19:38887400-38893200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr19:38887400-38893200	Weak transcription	NHEK	skin

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