Variant report

Variant	rs58591078
Chromosome Location	chr19:38884248-38884249
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	chr19:38871440-38886227	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr19:38883299-38886167	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38724585..38727174-chr19:38883492..38886224,2	K562	blood:
2	chr19:38864523..38867483-chr19:38883200..38885064,2	MCF-7	breast:

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

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10153497	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11880285	1.00[AMR][1000 genomes]
rs11881714	1.00[AMR][1000 genomes]
rs2286548	1.00[AMR][1000 genomes]
rs2302185	1.00[AMR][1000 genomes]
rs45589333	1.00[AMR][1000 genomes]
rs57249964	1.00[AMR][1000 genomes]
rs57347571	1.00[AMR][1000 genomes]
rs57361474	1.00[AMR][1000 genomes]
rs58247981	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58490212	1.00[AMR][1000 genomes]
rs59047386	1.00[AMR][1000 genomes]
rs59776537	1.00[AMR][1000 genomes]
rs59845491	1.00[AMR][1000 genomes]
rs60068553	1.00[AMR][1000 genomes]
rs60491875	1.00[AMR][1000 genomes]
rs61648033	1.00[AMR][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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38880000-38885200	Weak transcription	Pancreas	Pancrea
2	chr19:38880000-38886400	Weak transcription	Gastric	stomach
3	chr19:38880200-38884400	Weak transcription	Brain Hippocampus Middle	brain
4	chr19:38880200-38885000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:38880200-38885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:38880200-38885000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:38880200-38885200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:38880200-38885400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:38880200-38887600	Weak transcription	Right Atrium	heart
10	chr19:38880400-38885000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:38880400-38885000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:38880800-38889200	Weak transcription	Brain Angular Gyrus	brain
13	chr19:38881000-38884400	Weak transcription	Brain Anterior Caudate	brain
14	chr19:38881000-38885000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr19:38881000-38885200	Weak transcription	NHEK	skin
16	chr19:38881000-38887000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr19:38881000-38887600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:38881000-38893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:38881000-38893200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:38881000-38893200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr19:38881000-38893200	Weak transcription	HSMMtube	muscle
22	chr19:38881200-38887200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:38881600-38886200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:38882200-38884600	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr19:38882200-38885000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:38882400-38884600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:38882400-38885200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:38882600-38888000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:38882800-38884600	Enhancers	Fetal Intestine Large	intestine
30	chr19:38882800-38887400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:38883000-38885400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:38883000-38885400	Enhancers	Fetal Intestine Small	intestine
33	chr19:38883000-38888000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:38883200-38884600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:38883200-38884800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr19:38883200-38884800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:38883200-38885400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:38883200-38887800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:38883600-38885400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:38883600-38885600	Enhancers	Duodenum Mucosa	Duodenum
41	chr19:38883600-38891600	Weak transcription	HUVEC	blood vessel
42	chr19:38883600-38893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:38883800-38884400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr19:38883800-38884400	Weak transcription	HSMM	muscle
45	chr19:38883800-38884400	Weak transcription	NH-A	brain
46	chr19:38883800-38884600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr19:38883800-38884600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:38883800-38884600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:38883800-38884800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:38883800-38885000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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