Variant report

Variant	rs2967506
Chromosome Location	chr19:36856251-36856252
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10404574	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10409091	0.95[CHB][hapmap]
rs10414054	0.92[ASN][1000 genomes]
rs10418510	0.87[ASW][hapmap];0.95[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];0.96[ASN][1000 genomes]
rs10420071	0.80[CHB][hapmap];0.80[MKK][hapmap]
rs10420610	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10439091	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12459465	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12971694	0.92[ASN][1000 genomes]
rs12976881	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2070132	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[MEX][hapmap]
rs2271844	0.87[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2287897	0.95[CHB][hapmap];0.81[MEX][hapmap]
rs2287898	0.95[CHB][hapmap];0.81[MEX][hapmap]
rs2385799	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2385800	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2385801	0.87[ASW][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap]
rs2385803	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2385804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2385805	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2432039	0.95[CHB][hapmap]
rs2432045	0.95[CHB][hapmap];0.80[CHD][hapmap];0.81[MEX][hapmap]
rs2432049	0.95[CHB][hapmap]
rs2432054	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[MEX][hapmap]
rs2438514	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[MEX][hapmap]
rs2438517	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[MEX][hapmap]
rs2918349	0.90[ASN][1000 genomes]
rs2945945	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];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2945949	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2945950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2945951	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2945957	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2945961	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]
rs2945963	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2945971	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2945972	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];0.97[ASN][1000 genomes]
rs2945985	0.87[ASW][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap]
rs2945992	0.93[ASN][1000 genomes]
rs2945993	0.87[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2945994	0.87[ASN][1000 genomes]
rs2945995	0.95[ASN][1000 genomes]
rs2967484	0.87[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap];0.89[ASN][1000 genomes]
rs2967493	0.86[ASN][1000 genomes]
rs2967496	0.86[ASN][1000 genomes]
rs2967501	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2967504	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2967509	0.96[ASN][1000 genomes]
rs2967510	0.97[ASN][1000 genomes]
rs2967512	0.95[ASN][1000 genomes]
rs2967515	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2967517	0.87[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][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]
rs2967518	0.87[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2967521	0.81[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2967523	0.91[ASN][1000 genomes]
rs2967524	0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.93[ASN][1000 genomes]
rs2972632	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972633	0.91[ASN][1000 genomes]
rs4239585	0.95[CHB][hapmap]
rs4806321	0.88[ASN][1000 genomes]
rs5021030	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58703752	0.84[ASN][1000 genomes]
rs62112565	0.88[ASN][1000 genomes]
rs6417185	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6510541	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6510542	0.92[ASN][1000 genomes]
rs7246106	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs7251979	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7255260	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7255403	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8102020	0.95[CHB][hapmap];0.81[MEX][hapmap]
rs8106095	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109320	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8109333	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8112312	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8182628	0.82[AFR][1000 genomes];0.82[AMR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2967506	ZFP14	cis	Lymphoblastoid	GTEx
rs2967506	SPINT2	cis	cerebellum	SCAN
rs2967506	LOC284412	N/A	lymphoblastoid	RTeQTL
rs2967506	LINC00665	cis	Muscle Skeletal	GTEx
rs2967506	ZNF527	cis	cerebellum	SCAN
rs2967506	LINC00665	cis	Thyroid	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36827200-36862200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:36830600-36869400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:36832200-36868600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:36834000-36857400	Weak transcription	Brain Substantia Nigra	brain
5	chr19:36834200-36868800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr19:36835800-36857200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:36835800-36868800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:36836400-36858400	Weak transcription	Osteobl	bone
9	chr19:36836400-36868000	Weak transcription	Psoas Muscle	Psoas
10	chr19:36836600-36857200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:36836600-36863400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:36838000-36868600	Weak transcription	Stomach Mucosa	stomach
13	chr19:36842400-36861200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:36844200-36868800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:36845200-36858200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:36845800-36859200	Weak transcription	Fetal Thymus	thymus
17	chr19:36846600-36866400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:36847200-36859200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr19:36847200-36859800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr19:36847400-36862200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
21	chr19:36848200-36860200	Weak transcription	NHDF-Ad	bronchial
22	chr19:36848400-36861000	Weak transcription	NH-A	brain
23	chr19:36848800-36862000	Weak transcription	Hela-S3	cervix
24	chr19:36850000-36857200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:36850000-36868000	Weak transcription	Fetal Heart	heart
26	chr19:36850400-36859200	Strong transcription	Fetal Intestine Large	intestine
27	chr19:36850800-36862000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr19:36851400-36857600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr19:36851800-36856400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:36851800-36857200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:36851800-36857400	Weak transcription	HSMMtube	muscle
32	chr19:36851800-36863600	Weak transcription	Fetal Kidney	kidney
33	chr19:36852200-36867600	Weak transcription	HepG2	liver
34	chr19:36852800-36856400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
35	chr19:36853200-36856400	Weak transcription	Colon Smooth Muscle	Colon
36	chr19:36853200-36857000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:36853200-36857200	Weak transcription	Placenta	Placenta
38	chr19:36853200-36857600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr19:36853400-36857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:36853400-36857400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:36853400-36857400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr19:36853400-36857400	Weak transcription	Small Intestine	intestine
43	chr19:36854200-36856800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:36854200-36858600	ZNF genes & repeats	Thymus	Thymus
45	chr19:36854200-36859800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:36854400-36857000	ZNF genes & repeats	Primary B cells from cord blood	blood
47	chr19:36854400-36857800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:36854400-36858000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr19:36854400-36858400	Strong transcription	Brain Hippocampus Middle	brain
50	chr19:36854400-36859000	ZNF genes & repeats	A549	lung

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