Variant report

Variant	rs61162240
Chromosome Location	chr19:38883797-38883798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000099341	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11083455	0.82[AMR][1000 genomes]
rs11880532	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12608722	0.85[EUR][1000 genomes]
rs12609878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041221	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2074981	0.84[AFR][1000 genomes]
rs3745958	0.83[EUR][1000 genomes]
rs3745959	0.83[EUR][1000 genomes]
rs57146784	0.82[EUR][1000 genomes]
rs6508790	0.82[EUR][1000 genomes]
rs73044940	0.87[AFR][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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38879600-38884000	Enhancers	K562	blood
2	chr19:38880000-38885200	Weak transcription	Pancreas	Pancrea
3	chr19:38880000-38886400	Weak transcription	Gastric	stomach
4	chr19:38880200-38884400	Weak transcription	Brain Hippocampus Middle	brain
5	chr19:38880200-38885000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:38880200-38885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:38880200-38885000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:38880200-38885200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:38880200-38885400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:38880200-38887600	Weak transcription	Right Atrium	heart
11	chr19:38880400-38884000	Enhancers	A549	lung
12	chr19:38880400-38885000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:38880400-38885000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr19:38880600-38884000	Weak transcription	Psoas Muscle	Psoas
15	chr19:38880800-38889200	Weak transcription	Brain Angular Gyrus	brain
16	chr19:38881000-38884400	Weak transcription	Brain Anterior Caudate	brain
17	chr19:38881000-38885000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr19:38881000-38885200	Weak transcription	NHEK	skin
19	chr19:38881000-38887000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:38881000-38887600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:38881000-38893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:38881000-38893200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr19:38881000-38893200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr19:38881000-38893200	Weak transcription	HSMMtube	muscle
25	chr19:38881200-38887200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:38881400-38883800	Genic enhancers	NHLF	lung
27	chr19:38881600-38886200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:38882200-38884600	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr19:38882200-38885000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:38882400-38883800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:38882400-38883800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr19:38882400-38883800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:38882400-38883800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:38882400-38883800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:38882400-38884000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr19:38882400-38884000	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr19:38882400-38884600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:38882400-38885200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr19:38882600-38883800	Genic enhancers	NHDF-Ad	bronchial
40	chr19:38882600-38883800	Genic enhancers	Osteobl	bone
41	chr19:38882600-38884000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:38882600-38884000	Strong transcription	Aorta	Aorta
43	chr19:38882600-38888000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:38882800-38883800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:38882800-38883800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:38882800-38884600	Enhancers	Fetal Intestine Large	intestine
47	chr19:38882800-38887400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr19:38883000-38883800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr19:38883000-38883800	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:38883000-38884000	Enhancers	HepG2	liver

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