Variant report

Variant	rs2945963
Chromosome Location	chr19:36886705-36886706
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10402405	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10404574	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10414054	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10418510	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420610	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426014	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10439091	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12459465	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12971694	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12976881	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271844	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385799	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385800	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385801	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2385803	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385805	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918349	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2945945	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945948	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945949	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945950	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945951	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945957	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945961	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945971	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945972	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945992	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945993	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2945994	0.90[ASN][1000 genomes]
rs2945995	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2967484	0.85[ASN][1000 genomes]
rs2967493	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2967496	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2967501	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967504	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967506	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2967509	0.96[ASN][1000 genomes]
rs2967510	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967512	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2967515	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967517	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967518	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967521	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967523	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967524	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967526	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2967543	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2972633	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4806321	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5021030	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58703752	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62112565	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6417185	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6510541	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6510542	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246106	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7251979	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255260	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255403	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8106095	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8109320	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109333	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112312	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8182628	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1066026	chr19:36878441-36947928	ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2945963	LOC284412	N/A	lymphoblastoid	RTeQTL
rs2945963	LINC00665	cis	Muscle Skeletal	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36880400-36887400	ZNF genes & repeats	Brain Germinal Matrix	brain
2	chr19:36880400-36892800	ZNF genes & repeats	Liver	Liver
3	chr19:36880400-36893200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:36880400-36904600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:36880600-36889000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
6	chr19:36880600-36893000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
7	chr19:36880600-36893200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:36880800-36888400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:36881400-36892800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:36882000-36887400	ZNF genes & repeats	A549	lung
11	chr19:36882000-36891800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
12	chr19:36882200-36886800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
13	chr19:36882200-36888800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
14	chr19:36882200-36890400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr19:36882200-36892800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr19:36882200-36908800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:36882400-36887000	ZNF genes & repeats	Colon Smooth Muscle	Colon
18	chr19:36882400-36887400	ZNF genes & repeats	Aorta	Aorta
19	chr19:36882400-36887800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:36882400-36887800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:36882400-36888800	ZNF genes & repeats	Left Ventricle	heart
22	chr19:36882400-36890600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:36882400-36892000	ZNF genes & repeats	Fetal Brain Female	brain
24	chr19:36882400-36892800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:36882400-36896600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:36882400-36907600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:36882600-36887200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
28	chr19:36882600-36887400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr19:36882600-36887800	ZNF genes & repeats	Fetal Lung	lung
30	chr19:36882600-36888600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:36882600-36888800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
32	chr19:36882600-36888800	ZNF genes & repeats	Fetal Muscle Leg	muscle
33	chr19:36882600-36889600	ZNF genes & repeats	Fetal Intestine Large	intestine
34	chr19:36882600-36890400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:36882600-36893600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr19:36882600-36904200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:36882800-36886800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
38	chr19:36882800-36887400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:36882800-36887400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
40	chr19:36882800-36888400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
41	chr19:36882800-36888800	ZNF genes & repeats	Lung	lung
42	chr19:36882800-36893000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:36883000-36887000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
44	chr19:36883000-36888800	ZNF genes & repeats	Thymus	Thymus
45	chr19:36883000-36888800	ZNF genes & repeats	Dnd41	blood
46	chr19:36883000-36890600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:36883000-36892800	ZNF genes & repeats	Ovary	ovary
48	chr19:36883000-36893000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:36883000-36893400	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr19:36883000-36905200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood

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