Variant report

Variant	rs262529
Chromosome Location	chr2:63903892-63903893
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63902199..63904548-chr2:63905290..63907051,2	MCF-7	breast:

Extended variants
information (count: 178 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:177)

rs_ID	r²[population]
rs10168545	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10170988	0.80[AMR][1000 genomes]
rs10171223	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10176522	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1023820	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10469944	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10469945	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1082363	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865337	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10865338	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10865339	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865341	0.80[AMR][1000 genomes]
rs11125977	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11125978	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs112194	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11693909	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11898615	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12105140	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1255	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713494	0.80[EUR][1000 genomes]
rs12713496	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12990914	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1348803	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348805	0.87[EUR][1000 genomes]
rs1348806	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1356390	0.87[AMR][1000 genomes]
rs1374308	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446563	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446564	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1446565	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1446569	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1550860	0.85[EUR][1000 genomes]
rs166384	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs166385	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171901	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174485	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs185499	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867847	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1867849	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs187801	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1900303	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs190519	0.87[EUR][1000 genomes]
rs196123	0.90[ASN][1000 genomes]
rs196124	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs196125	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2028883	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2028887	0.82[EUR][1000 genomes]
rs2084200	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2121350	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2121351	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2121353	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166494	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2166497	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2292793	0.82[AMR][1000 genomes]
rs2305157	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2422011	0.85[EUR][1000 genomes]
rs2592386	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592387	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592388	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2604613	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2604614	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2604615	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2604617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs262470	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262471	0.83[EUR][1000 genomes]
rs262472	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262473	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262474	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262475	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262476	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262477	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262478	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262479	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs262480	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262481	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262482	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262483	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262484	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262485	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262486	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262487	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262488	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262489	0.83[EUR][1000 genomes]
rs262490	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262491	0.90[ASN][1000 genomes]
rs262492	0.90[ASN][1000 genomes]
rs262493	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262494	0.90[ASN][1000 genomes]
rs262495	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262501	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262502	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262503	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262504	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262505	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262506	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262507	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262508	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262509	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262510	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs262511	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262512	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262513	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs262514	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262515	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262516	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262517	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262518	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262519	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262520	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262521	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262523	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262524	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs262525	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262526	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262527	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262531	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262532	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs262533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262534	1.00[ASN][1000 genomes]
rs262535	1.00[ASN][1000 genomes]
rs262536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262537	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262539	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901614	0.86[EUR][1000 genomes]
rs3980466	0.81[AMR][1000 genomes]
rs4255949	0.81[AMR][1000 genomes]
rs4671065	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671067	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4671068	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671069	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671505	0.80[AMR][1000 genomes]
rs4671508	0.80[AMR][1000 genomes]
rs4671509	0.81[AMR][1000 genomes]
rs4671512	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4671514	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4671515	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4671516	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4671517	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4671519	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6546005	0.85[AMR][1000 genomes]
rs6546007	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6546009	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6546011	0.86[AMR][1000 genomes]
rs6546016	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6546017	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6546018	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6546019	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6706123	0.85[EUR][1000 genomes]
rs6708804	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6717031	0.85[EUR][1000 genomes]
rs6724160	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6732791	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6734648	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6736029	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6738190	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6754730	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs68183503	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7563623	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7570031	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7571017	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7571325	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7576316	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7577952	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7584404	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7606045	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7607257	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7608470	0.81[AMR][1000 genomes]
rs7608513	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs959195	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs964880	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs964903	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9789351	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs989527	0.87[AMR][1000 genomes];0.86[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	nsv834242	chr2:63891249-64045617	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs262529	MDH1	cis	Adipose Subcutaneous	GTEx
rs262529	WDPCP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63896400-63907200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:63896400-63911400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:63900400-63904000	Enhancers	Adipose Nuclei	Adipose
4	chr2:63901000-63907000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:63901400-63904200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:63901400-63907400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:63903200-63904000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:63903200-63904200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:63903200-63904200	Enhancers	Liver	Liver
10	chr2:63903200-63904400	Enhancers	GM12878-XiMat	blood
11	chr2:63903200-63904800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr2:63903400-63904000	Enhancers	Aorta	Aorta
13	chr2:63903400-63904000	Enhancers	Small Intestine	intestine
14	chr2:63903400-63905400	Enhancers	Primary T cells from cord blood	blood
15	chr2:63903600-63904000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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