Variant report

Variant	rs2945957
Chromosome Location	chr19:36892833-36892834
allele	C/T
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];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10404574	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10414054	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10418510	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420610	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426014	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10439091	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12459465	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12971694	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12976881	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271844	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385799	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385800	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385801	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2385803	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918349	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2945945	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945948	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945949	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945950	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945951	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945961	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945963	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945971	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945972	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945992	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945993	1.00[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	0.97[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[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2967501	0.86[AFR][1000 genomes];0.80[AMR][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[AFR][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	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967517	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967518	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967521	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967523	0.92[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	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2972633	0.85[AFR][1000 genomes];0.80[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	0.97[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	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6510541	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6510542	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246106	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7251979	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255260	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255403	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8106095	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs8109320	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109333	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112312	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8182628	0.96[AFR][1000 genomes];0.93[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
rs2945957	LINC00665	cis	Muscle Skeletal	GTEx
rs2945957	LOC284412	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36880400-36893200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:36880400-36904600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:36880600-36893000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
4	chr19:36880600-36893200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:36882200-36908800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:36882400-36896600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:36882400-36907600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:36882600-36893600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr19:36882600-36904200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:36882800-36893000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:36883000-36893000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:36883000-36893400	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr19:36883000-36905200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
14	chr19:36883600-36893800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
15	chr19:36885600-36908000	Weak transcription	K562	blood
16	chr19:36886200-36893800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:36886400-36901000	Weak transcription	Stomach Mucosa	stomach
18	chr19:36886600-36895200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:36886600-36895200	Weak transcription	Right Ventricle	heart
20	chr19:36886600-36898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:36886800-36895000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:36888400-36893600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:36888400-36893800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr19:36888400-36901200	Strong transcription	Brain Hippocampus Middle	brain
25	chr19:36888800-36893000	ZNF genes & repeats	Primary T cells from cord blood	blood
26	chr19:36888800-36893200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
27	chr19:36888800-36893600	Strong transcription	Thymus	Thymus
28	chr19:36888800-36893600	Strong transcription	Osteobl	bone
29	chr19:36888800-36895000	Weak transcription	Fetal Thymus	thymus
30	chr19:36889600-36893000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
31	chr19:36889600-36893200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:36889600-36893600	Strong transcription	Fetal Intestine Large	intestine
33	chr19:36889600-36900200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr19:36889800-36908200	Weak transcription	HepG2	liver
35	chr19:36890200-36893000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
36	chr19:36890400-36893200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:36890400-36893600	Strong transcription	Fetal Brain Male	brain
38	chr19:36890400-36893600	Strong transcription	NHDF-Ad	bronchial
39	chr19:36890400-36895000	Weak transcription	Colonic Mucosa	Colon
40	chr19:36890400-36901400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:36890600-36895000	Weak transcription	Pancreas	Pancrea
42	chr19:36890800-36893000	Strong transcription	Placenta	Placenta
43	chr19:36891000-36893000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
44	chr19:36891000-36893000	ZNF genes & repeats	Fetal Lung	lung
45	chr19:36891000-36896600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:36891000-36904800	Strong transcription	Dnd41	blood
47	chr19:36891200-36893000	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:36891200-36893000	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
49	chr19:36891200-36893000	Strong transcription	Colon Smooth Muscle	Colon
50	chr19:36891200-36898000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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