Variant report

Variant	rs440545
Chromosome Location	chr19:53033037-53033038
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	chr19:53031656..53034156-chr19:53037494..53039065,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs12462347	0.87[EUR][1000 genomes]
rs12463002	0.83[EUR][1000 genomes]
rs12974840	0.84[EUR][1000 genomes]
rs162277	0.91[EUR][1000 genomes]
rs162278	0.91[EUR][1000 genomes]
rs1676153	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2045754	0.90[ASN][1000 genomes]
rs2608513	0.82[ASN][1000 genomes]
rs2608522	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2608527	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2615586	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2615587	0.88[ASN][1000 genomes]
rs2615588	0.89[ASN][1000 genomes]
rs2617795	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2633502	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2633513	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2633514	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2633517	0.96[ASN][1000 genomes]
rs2925976	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs326440	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs326441	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs326442	0.83[EUR][1000 genomes]
rs326443	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs326444	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs326446	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs326447	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs326448	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs326449	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs326458	0.92[EUR][1000 genomes]
rs34222822	0.86[EUR][1000 genomes]
rs36039960	0.86[EUR][1000 genomes]
rs368922	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs369806	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs375267	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs376595	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs396663	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs400709	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs402737	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs410046	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs413751	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs413814	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs417599	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs422195	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs429367	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434709	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs434788	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs439618	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs441549	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs441850	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs445500	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs449671	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802965	0.81[EUR][1000 genomes]
rs4802971	0.96[ASN][1000 genomes]
rs4802972	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs520958	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs521703	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs529698	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs532449	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs606521	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs606538	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs606914	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs607477	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62117197	0.92[ASN][1000 genomes]
rs62117198	0.93[ASN][1000 genomes]
rs62117199	0.94[ASN][1000 genomes]
rs62119359	0.95[ASN][1000 genomes]
rs642493	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs653483	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs656541	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs666356	0.81[EUR][1000 genomes]
rs668882	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs685200	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs688646	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs781129	0.96[ASN][1000 genomes]
rs92520	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3404701	chr19:52986895-53035152	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3440535	chr19:52993529-53035203	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1055825	chr19:53001299-53037378	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53031600-53033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:53031800-53038600	Weak transcription	Aorta	Aorta
3	chr19:53031800-53038800	Weak transcription	Ovary	ovary
4	chr19:53032000-53033200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:53032000-53036000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:53032000-53037000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:53032000-53037200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr19:53032000-53038000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:53032000-53038200	Weak transcription	Fetal Lung	lung
10	chr19:53032000-53038400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:53032000-53038400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr19:53032000-53038400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr19:53032000-53038600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:53032000-53038600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr19:53032000-53038600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:53032000-53038600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr19:53032000-53038600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr19:53032000-53038600	Weak transcription	HMEC	breast
19	chr19:53032000-53038600	Weak transcription	HSMM	muscle
20	chr19:53032000-53038600	Weak transcription	HUVEC	blood vessel
21	chr19:53032000-53038600	Weak transcription	NH-A	brain
22	chr19:53032000-53038600	Weak transcription	NHDF-Ad	bronchial
23	chr19:53032000-53038600	Weak transcription	Osteobl	bone
24	chr19:53032000-53038800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr19:53032000-53038800	Weak transcription	Small Intestine	intestine
26	chr19:53032000-53039000	Weak transcription	HSMMtube	muscle
27	chr19:53032200-53033600	Weak transcription	Primary B cells from cord blood	blood
28	chr19:53032200-53036200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:53032200-53036200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr19:53032200-53036200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:53032200-53036200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:53032200-53036600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:53032200-53037200	Weak transcription	Colonic Mucosa	Colon
34	chr19:53032200-53037400	Weak transcription	Right Atrium	heart
35	chr19:53032200-53038000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:53032200-53038200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:53032200-53038200	Weak transcription	Brain Germinal Matrix	brain
38	chr19:53032200-53038600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:53032200-53038600	Weak transcription	NHLF	lung
40	chr19:53032200-53039400	Weak transcription	Stomach Mucosa	stomach
41	chr19:53032200-53057000	Weak transcription	Hela-S3	cervix
42	chr19:53032400-53033200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:53032400-53033800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:53032400-53036200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:53032400-53036200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr19:53032400-53036400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr19:53032400-53036600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:53032400-53037000	Weak transcription	Fetal Heart	heart
49	chr19:53032400-53038200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr19:53032400-53038200	Weak transcription	Primary T cells from cord blood	blood

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