Variant report

Variant	rs417599
Chromosome Location	chr19:53036339-53036340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs12462347	0.85[EUR][1000 genomes]
rs12463002	0.82[EUR][1000 genomes]
rs12974840	0.83[EUR][1000 genomes]
rs162277	0.90[EUR][1000 genomes]
rs162278	0.90[EUR][1000 genomes]
rs1676153	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2045754	0.89[ASN][1000 genomes]
rs2608513	0.85[ASN][1000 genomes]
rs2608522	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608527	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2615586	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2615587	0.90[ASN][1000 genomes]
rs2615588	0.92[ASN][1000 genomes]
rs2617795	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2633502	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2633513	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2633514	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2633517	0.97[ASN][1000 genomes]
rs2925976	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs326439	0.82[ASN][1000 genomes]
rs326440	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs326441	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs326442	0.86[EUR][1000 genomes]
rs326443	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs326444	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs326446	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs326447	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs326448	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs326449	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs326458	0.91[EUR][1000 genomes]
rs34222822	0.85[EUR][1000 genomes]
rs36039960	0.85[EUR][1000 genomes]
rs368922	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs369806	0.88[EUR][1000 genomes]
rs375267	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs376595	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs396663	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs400709	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs402737	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs410046	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs413751	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs413814	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs422195	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs429367	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs434709	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs434788	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs439618	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs440545	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs441549	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs441850	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs445500	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs449671	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802971	0.99[ASN][1000 genomes]
rs4802972	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520958	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs521703	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs529698	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs532449	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs606521	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs606538	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs606914	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs607477	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62117197	0.95[ASN][1000 genomes]
rs62117198	0.95[ASN][1000 genomes]
rs62117199	0.97[ASN][1000 genomes]
rs62119359	0.97[ASN][1000 genomes]
rs642493	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs653483	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs655580	0.81[ASN][1000 genomes]
rs656541	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs666356	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs668882	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs685200	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs688646	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs781129	0.99[ASN][1000 genomes]
rs92520	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][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	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	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
8	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
9	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
10	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
11	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:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53031800-53038600	Weak transcription	Aorta	Aorta
2	chr19:53031800-53038800	Weak transcription	Ovary	ovary
3	chr19:53032000-53037000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:53032000-53037200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr19:53032000-53038000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:53032000-53038200	Weak transcription	Fetal Lung	lung
7	chr19:53032000-53038400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:53032000-53038400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr19:53032000-53038400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr19:53032000-53038600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:53032000-53038600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:53032000-53038600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:53032000-53038600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr19:53032000-53038600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:53032000-53038600	Weak transcription	HMEC	breast
16	chr19:53032000-53038600	Weak transcription	HSMM	muscle
17	chr19:53032000-53038600	Weak transcription	HUVEC	blood vessel
18	chr19:53032000-53038600	Weak transcription	NH-A	brain
19	chr19:53032000-53038600	Weak transcription	NHDF-Ad	bronchial
20	chr19:53032000-53038600	Weak transcription	Osteobl	bone
21	chr19:53032000-53038800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr19:53032000-53038800	Weak transcription	Small Intestine	intestine
23	chr19:53032000-53039000	Weak transcription	HSMMtube	muscle
24	chr19:53032200-53036600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr19:53032200-53037200	Weak transcription	Colonic Mucosa	Colon
26	chr19:53032200-53037400	Weak transcription	Right Atrium	heart
27	chr19:53032200-53038000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:53032200-53038200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:53032200-53038200	Weak transcription	Brain Germinal Matrix	brain
30	chr19:53032200-53038600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:53032200-53038600	Weak transcription	NHLF	lung
32	chr19:53032200-53039400	Weak transcription	Stomach Mucosa	stomach
33	chr19:53032200-53057000	Weak transcription	Hela-S3	cervix
34	chr19:53032400-53036400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:53032400-53036600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:53032400-53037000	Weak transcription	Fetal Heart	heart
37	chr19:53032400-53038200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr19:53032400-53038200	Weak transcription	Primary T cells from cord blood	blood
39	chr19:53032400-53038200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:53032400-53038200	Weak transcription	Colon Smooth Muscle	Colon
41	chr19:53032400-53038600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr19:53032400-53038600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr19:53032400-53038600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr19:53032400-53038800	Weak transcription	Fetal Kidney	kidney
45	chr19:53032400-53038800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr19:53032600-53036400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr19:53032600-53036400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:53032600-53036400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr19:53032600-53036400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:53032600-53036400	Weak transcription	Placenta	Placenta

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