Variant report

Variant	rs1859494
Chromosome Location	chr7:38753322-38753323
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1017028	0.86[ASN][1000 genomes]
rs10242048	0.86[ASN][1000 genomes]
rs10247503	0.90[ASN][1000 genomes]
rs10251912	0.90[ASN][1000 genomes]
rs10254567	0.90[ASN][1000 genomes]
rs10271176	0.90[ASN][1000 genomes]
rs10486677	0.88[ASN][1000 genomes]
rs10486678	0.88[ASN][1000 genomes]
rs11971020	0.88[ASN][1000 genomes]
rs11979618	0.97[ASN][1000 genomes]
rs11979824	0.88[ASN][1000 genomes]
rs12533557	0.90[ASN][1000 genomes]
rs12667567	0.87[ASN][1000 genomes]
rs12672237	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12672750	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12672793	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12672885	0.88[ASN][1000 genomes]
rs12701659	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1468348	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17700072	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17700142	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17700172	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17700190	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17700262	0.88[ASN][1000 genomes]
rs17700392	0.88[ASN][1000 genomes]
rs17767695	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17767770	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17767818	0.97[ASN][1000 genomes]
rs17768153	0.87[ASN][1000 genomes]
rs17768212	0.88[ASN][1000 genomes]
rs1978171	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1978172	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074655	0.88[ASN][1000 genomes]
rs2074657	0.88[ASN][1000 genomes]
rs2107743	0.90[ASN][1000 genomes]
rs2189855	0.88[ASN][1000 genomes]
rs2214666	0.88[ASN][1000 genomes]
rs2240351	0.90[ASN][1000 genomes]
rs2240352	0.89[ASN][1000 genomes]
rs2240353	0.88[ASN][1000 genomes]
rs2240354	0.87[ASN][1000 genomes]
rs2286082	0.88[ASN][1000 genomes]
rs2286084	0.88[ASN][1000 genomes]
rs2286087	0.88[ASN][1000 genomes]
rs2286088	0.88[ASN][1000 genomes]
rs2286091	0.88[ASN][1000 genomes]
rs2286094	0.88[ASN][1000 genomes]
rs2286098	0.88[ASN][1000 genomes]
rs2286104	0.88[ASN][1000 genomes]
rs2286105	0.88[ASN][1000 genomes]
rs2286106	0.90[ASN][1000 genomes]
rs2286109	0.97[ASN][1000 genomes]
rs2392598	0.90[ASN][1000 genomes]
rs28548028	0.90[ASN][1000 genomes]
rs35253728	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35791079	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735347	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3801139	0.89[ASN][1000 genomes]
rs3801140	0.89[ASN][1000 genomes]
rs3801141	0.88[ASN][1000 genomes]
rs3801143	0.90[ASN][1000 genomes]
rs3801145	0.88[ASN][1000 genomes]
rs3801146	0.90[ASN][1000 genomes]
rs4723782	0.90[ASN][1000 genomes]
rs4723785	0.90[ASN][1000 genomes]
rs56050717	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs57091471	0.88[ASN][1000 genomes]
rs60590111	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs62444078	0.87[ASN][1000 genomes]
rs62444107	0.88[ASN][1000 genomes]
rs6462860	0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs66662538	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs66796288	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66976998	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs67202646	0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs733150	0.90[ASN][1000 genomes]
rs73368205	0.86[ASN][1000 genomes]
rs7778570	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7779329	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7783546	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785911	0.90[ASN][1000 genomes]
rs7786389	0.88[ASN][1000 genomes]
rs7794030	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7795874	0.88[ASN][1000 genomes]
rs7797871	0.99[ASN][1000 genomes]
rs886646	0.90[ASN][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	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1859494	VPS41	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38748800-38756200	Weak transcription	Fetal Brain Female	brain
2	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
3	chr7:38753200-38754200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links