Variant report

Variant	rs262539
Chromosome Location	chr2:63908270-63908271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS54-6	chr2:63908260-63908444	l_1845_chr2:63834528-63908444_heart

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10170988	0.81[AMR][1000 genomes]
rs10469944	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10469945	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1082363	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865338	0.81[AMR][1000 genomes]
rs10865339	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs112194	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12990914	0.81[AMR][1000 genomes]
rs1348803	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348806	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374308	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446563	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446564	0.81[AMR][1000 genomes]
rs1446565	0.81[AMR][1000 genomes]
rs1446569	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs166384	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs166385	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171901	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171902	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174485	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs185499	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs187801	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1900303	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs196123	0.90[ASN][1000 genomes]
rs196124	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs196125	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2121351	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2121353	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166497	0.81[AMR][1000 genomes]
rs2305157	0.90[ASN][1000 genomes]
rs2592386	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592387	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592388	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2604613	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2604614	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2604615	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2604617	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs262470	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262472	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262473	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262475	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262476	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262477	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262478	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262479	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs262480	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262481	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262482	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262483	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262484	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262485	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262487	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262488	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262490	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262491	0.90[ASN][1000 genomes]
rs262492	0.90[ASN][1000 genomes]
rs262493	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262494	0.90[ASN][1000 genomes]
rs262495	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262501	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262502	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262503	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262504	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262505	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262506	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262507	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs262508	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262509	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262510	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs262511	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262512	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262513	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs262514	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262515	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262516	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262517	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262518	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262519	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262520	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262521	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262523	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262524	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs262525	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262526	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262527	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262528	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262529	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262530	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262532	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs262533	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262534	1.00[ASN][1000 genomes]
rs262535	1.00[ASN][1000 genomes]
rs262536	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262537	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262538	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671065	0.81[AMR][1000 genomes]
rs4671067	0.81[AMR][1000 genomes]
rs4671068	0.83[AMR][1000 genomes]
rs4671069	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671505	0.81[AMR][1000 genomes]
rs4671508	0.81[AMR][1000 genomes]
rs4671516	0.81[AMR][1000 genomes]
rs4671519	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6546009	0.81[AMR][1000 genomes]
rs6546017	0.81[AMR][1000 genomes]
rs6546018	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6546019	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6708804	0.82[AMR][1000 genomes]
rs6732791	0.81[AMR][1000 genomes]
rs6734648	0.81[AMR][1000 genomes]
rs6736029	0.81[AMR][1000 genomes]
rs68183503	0.81[AMR][1000 genomes]
rs7571017	0.81[AMR][1000 genomes]
rs7571325	0.81[AMR][1000 genomes]
rs7577952	0.81[AMR][1000 genomes]
rs7584404	0.81[AMR][1000 genomes]
rs7606045	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs964880	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs964903	0.81[AMR][1000 genomes]
rs9789351	0.81[AMR][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
rs262539	WDPCP	cis	Adipose Subcutaneous	GTEx
rs262539	MDH1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63896400-63911400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:63905600-63909200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:63905800-63909200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:63906400-63908800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:63907000-63908400	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr2:63907000-63908600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:63907200-63908400	Weak transcription	NHEK	skin
8	chr2:63907400-63908800	Enhancers	Adipose Nuclei	Adipose
9	chr2:63907400-63909200	Enhancers	Psoas Muscle	Psoas
10	chr2:63907600-63908400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:63907800-63908600	Enhancers	Placenta	Placenta
12	chr2:63907800-63909000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:63908200-63908400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:63908200-63909200	Enhancers	Skeletal Muscle Male	skeletal muscle

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