Variant report

Variant	rs6546016
Chromosome Location	chr2:63785434-63785435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 167 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs10168545	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10170988	0.84[EUR][1000 genomes]
rs10171223	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10176522	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1023820	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10469944	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10469945	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1082363	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10865337	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10865338	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865339	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865341	0.80[EUR][1000 genomes]
rs11125977	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11125978	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs112194	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11693909	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11898615	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12105140	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1255	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12713494	0.84[EUR][1000 genomes]
rs12713496	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12990914	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1348803	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1348806	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1356390	0.85[EUR][1000 genomes]
rs1374308	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1446563	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1446564	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1446565	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1446569	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1550860	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs166384	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs166385	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs171901	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs171902	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs174485	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs185499	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1867847	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1867849	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs187801	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs190519	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs196124	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs196125	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2028883	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2028887	0.89[EUR][1000 genomes]
rs2084200	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2121350	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2121351	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2121353	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2166494	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2166497	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2292793	0.83[EUR][1000 genomes]
rs2305157	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2422011	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2592386	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2592387	0.81[AMR][1000 genomes]
rs2592388	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2604613	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2604614	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2604617	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs262470	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs262471	0.89[EUR][1000 genomes]
rs262472	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262473	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs262474	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262475	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262476	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262477	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262478	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262479	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262480	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262481	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262482	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262483	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262484	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262485	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262486	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262487	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262488	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262489	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262490	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262493	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs262495	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs262501	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262502	0.86[EUR][1000 genomes]
rs262503	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262504	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262505	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262506	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262507	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262508	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262509	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs262510	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262514	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262515	0.81[AMR][1000 genomes]
rs262516	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262518	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262519	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262520	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262521	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262523	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs262524	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262525	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs262526	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262527	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262528	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs262529	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs262530	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs262533	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs262536	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs262538	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2901614	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3980466	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4255949	0.81[EUR][1000 genomes]
rs4671064	0.82[EUR][1000 genomes]
rs4671065	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671066	0.81[EUR][1000 genomes]
rs4671067	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4671068	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4671069	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4671503	0.82[EUR][1000 genomes]
rs4671505	0.84[EUR][1000 genomes]
rs4671508	0.84[EUR][1000 genomes]
rs4671509	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4671512	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4671514	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671515	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671516	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671517	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4671519	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6546004	0.82[EUR][1000 genomes]
rs6546005	0.83[EUR][1000 genomes]
rs6546007	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6546009	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6546011	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6546017	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6546018	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6546019	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6706123	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6708804	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6717031	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6724160	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6732791	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6734648	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6736029	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6736411	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6738190	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6754730	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs68183503	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7563623	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7570031	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7571017	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7571325	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7576316	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7577952	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7581630	0.84[EUR][1000 genomes]
rs7584404	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7606045	0.87[EUR][1000 genomes]
rs7607257	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7608470	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7608513	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs959195	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs964880	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs964903	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9789351	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs989527	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6546016	MDH1	cis	Adipose Subcutaneous	GTEx
rs6546016	WDPCP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63772800-63788800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:63777400-63806800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:63778800-63794000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:63780200-63786000	Weak transcription	Fetal Lung	lung
5	chr2:63780200-63814800	Weak transcription	Psoas Muscle	Psoas
6	chr2:63780400-63785800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr2:63780600-63785800	Weak transcription	Adipose Nuclei	Adipose
8	chr2:63780800-63791800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:63780800-63792200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:63781000-63793200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:63781000-63804000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:63781200-63790000	Weak transcription	Right Ventricle	heart
13	chr2:63781600-63785600	Weak transcription	Brain Anterior Caudate	brain
14	chr2:63781600-63786600	Weak transcription	Brain Angular Gyrus	brain
15	chr2:63781800-63787000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:63782600-63793400	Weak transcription	Lung	lung
17	chr2:63783000-63785600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:63783000-63789000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:63783400-63788800	Weak transcription	Primary T cells from cord blood	blood
20	chr2:63783400-63798600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:63783600-63790600	Weak transcription	Liver	Liver
22	chr2:63783600-63793800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:63783800-63787200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:63783800-63788800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:63783800-63790000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:63785400-63786200	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links