Variant report

Variant	rs2945971
Chromosome Location	chr19:36853523-36853524
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10402405	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10404574	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10414054	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10418510	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420610	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10426014	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10439091	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12459465	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971694	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12976881	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2271844	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385799	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2385800	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2385801	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2385803	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2385805	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2918349	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2945945	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945948	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2945949	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945950	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945951	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945957	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945961	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945963	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945972	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945992	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2945993	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2945994	0.87[ASN][1000 genomes]
rs2945995	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967484	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967493	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967496	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967501	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967504	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967506	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2967509	0.96[ASN][1000 genomes]
rs2967510	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967512	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967515	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967517	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967518	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967521	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967523	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2967524	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967526	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2967543	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2972632	0.82[ASN][1000 genomes]
rs2972633	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4806321	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5021030	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58703752	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62112565	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6417185	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6510541	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6510542	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7246106	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7251979	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7255260	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255403	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106095	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8109320	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109333	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112312	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8182628	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv2474	chr19:36804469-36865415	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	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
3	nsv174	chr19:36831719-36865415	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv579459	chr19:36845537-36856379	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2945971	LOC284412	N/A	lymphoblastoid	RTeQTL
rs2945971	LINC00665	cis	Muscle Skeletal	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36823800-36853600	ZNF genes & repeats	Liver	Liver
2	chr19:36827200-36862200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:36830600-36869400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:36832200-36868600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:36834000-36857400	Weak transcription	Brain Substantia Nigra	brain
6	chr19:36834200-36868800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr19:36835800-36857200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:36835800-36868800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr19:36836400-36858400	Weak transcription	Osteobl	bone
10	chr19:36836400-36868000	Weak transcription	Psoas Muscle	Psoas
11	chr19:36836600-36857200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:36836600-36863400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:36838000-36868600	Weak transcription	Stomach Mucosa	stomach
14	chr19:36838200-36855000	Weak transcription	HSMM	muscle
15	chr19:36840000-36855000	Weak transcription	Right Ventricle	heart
16	chr19:36840000-36856000	Weak transcription	Fetal Lung	lung
17	chr19:36841200-36854800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:36842400-36861200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:36844200-36868800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:36845200-36858200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:36845800-36859200	Weak transcription	Fetal Thymus	thymus
22	chr19:36846000-36855000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:36846600-36866400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:36847200-36853600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr19:36847200-36859200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:36847200-36859800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr19:36847400-36853600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:36847400-36862200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
29	chr19:36847600-36855800	Weak transcription	Fetal Muscle Leg	muscle
30	chr19:36848200-36860200	Weak transcription	NHDF-Ad	bronchial
31	chr19:36848400-36861000	Weak transcription	NH-A	brain
32	chr19:36848800-36862000	Weak transcription	Hela-S3	cervix
33	chr19:36849400-36853600	Strong transcription	Primary T cells from cord blood	blood
34	chr19:36849400-36853600	Strong transcription	Fetal Brain Female	brain
35	chr19:36849800-36853800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr19:36850000-36854800	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr19:36850000-36855000	Weak transcription	Colonic Mucosa	Colon
38	chr19:36850000-36857200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr19:36850000-36868000	Weak transcription	Fetal Heart	heart
40	chr19:36850200-36855000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr19:36850400-36859200	Strong transcription	Fetal Intestine Large	intestine
42	chr19:36850800-36862000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr19:36851000-36854400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:36851200-36853600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
45	chr19:36851400-36855000	Weak transcription	Esophagus	oesophagus
46	chr19:36851400-36855000	Weak transcription	Pancreas	Pancrea
47	chr19:36851400-36857600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:36851600-36854200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr19:36851600-36856000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:36851800-36855000	Weak transcription	Left Ventricle	heart

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