Variant report

Variant	rs2945961
Chromosome Location	chr19:36883444-36883445
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10402043	0.82[GIH][hapmap]
rs10402405	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10404574	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10409091	0.95[CHB][hapmap]
rs10414054	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10418510	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420071	0.86[ASW][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.88[LWK][hapmap];0.88[MKK][hapmap]
rs10420610	0.97[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	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12459465	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12971694	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12976881	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070132	0.90[CHB][hapmap];0.91[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs2271844	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287897	0.95[CHB][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2287898	0.95[CHB][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2385799	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385800	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385801	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2385803	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2385805	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432039	0.90[CHB][hapmap]
rs2432045	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs2432049	0.90[CHB][hapmap]
rs2432054	0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs2438514	0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs2438517	0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs2918349	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2945945	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945948	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945949	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945951	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945957	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945963	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945971	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945985	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs2945992	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[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	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2967484	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2967493	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2967496	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2967501	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967504	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967506	0.87[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967517	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967518	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967521	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967523	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967524	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967526	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2967543	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2972633	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4239585	0.90[CHB][hapmap]
rs4806321	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5021030	0.95[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[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6417185	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6510541	0.89[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	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7251979	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255260	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255403	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102020	0.95[CHB][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs8106095	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8109320	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109333	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112312	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8182628	0.98[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2945961	LINC00665	cis	Muscle Skeletal	GTEx
rs2945961	ZNF527	cis	cerebellum	SCAN
rs2945961	LOC284412	N/A	lymphoblastoid	RTeQTL
rs2945961	TMEM91	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

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	chr19:36880600-36886600	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:36880600-36889000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
7	chr19:36880600-36893000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
8	chr19:36880600-36893200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:36880800-36886600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
10	chr19:36880800-36888400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr19:36881000-36886600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
12	chr19:36881400-36892800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:36882000-36887400	ZNF genes & repeats	A549	lung
14	chr19:36882000-36891800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
15	chr19:36882200-36886200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:36882200-36886600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
17	chr19:36882200-36886600	ZNF genes & repeats	Psoas Muscle	Psoas
18	chr19:36882200-36886800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
19	chr19:36882200-36888800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr19:36882200-36890400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
21	chr19:36882200-36892800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr19:36882200-36908800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:36882400-36884800	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
24	chr19:36882400-36886200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
25	chr19:36882400-36886600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
26	chr19:36882400-36886600	ZNF genes & repeats	Primary T cells from cord blood	blood
27	chr19:36882400-36886600	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
28	chr19:36882400-36886600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
29	chr19:36882400-36886600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
30	chr19:36882400-36886600	ZNF genes & repeats	HSMMtube	muscle
31	chr19:36882400-36887000	ZNF genes & repeats	Colon Smooth Muscle	Colon
32	chr19:36882400-36887400	ZNF genes & repeats	Aorta	Aorta
33	chr19:36882400-36887800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:36882400-36887800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:36882400-36888800	ZNF genes & repeats	Left Ventricle	heart
36	chr19:36882400-36890600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:36882400-36892000	ZNF genes & repeats	Fetal Brain Female	brain
38	chr19:36882400-36892800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:36882400-36896600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:36882400-36907600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:36882600-36886600	ZNF genes & repeats	Primary B cells from cord blood	blood
42	chr19:36882600-36886600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr19:36882600-36886600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
44	chr19:36882600-36886600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
45	chr19:36882600-36887200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
46	chr19:36882600-36887400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr19:36882600-36887800	ZNF genes & repeats	Fetal Lung	lung
48	chr19:36882600-36888600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr19:36882600-36888800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
50	chr19:36882600-36888800	ZNF genes & repeats	Fetal Muscle Leg	muscle

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