Variant report

Variant	rs1914723
Chromosome Location	chr11:93760506-93760507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VSTM5-3	chr11:93760135-93761825	NONHSAT023702

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11020619	0.83[EUR][1000 genomes]
rs11820915	0.96[EUR][1000 genomes]
rs11823303	0.98[EUR][1000 genomes]
rs11823785	0.87[EUR][1000 genomes]
rs11823836	0.89[EUR][1000 genomes]
rs11828737	0.96[EUR][1000 genomes]
rs12278077	0.85[EUR][1000 genomes]
rs12279295	0.86[ASN][1000 genomes]
rs1518560	0.83[EUR][1000 genomes]
rs1518565	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1518566	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1518573	0.91[EUR][1000 genomes]
rs1568259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919810	0.98[EUR][1000 genomes]
rs16919815	1.00[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.98[EUR][1000 genomes]
rs16919858	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1850656	0.83[EUR][1000 genomes]
rs1894166	0.80[EUR][1000 genomes]
rs1945786	0.83[EUR][1000 genomes]
rs1945787	0.83[EUR][1000 genomes]
rs2020351	0.80[EUR][1000 genomes]
rs2139089	0.83[EUR][1000 genomes]
rs2213108	0.81[EUR][1000 genomes]
rs2399749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399750	0.83[EUR][1000 genomes]
rs2460049	0.83[EUR][1000 genomes]
rs2460050	0.83[EUR][1000 genomes]
rs2460058	0.90[EUR][1000 genomes]
rs2460064	0.81[EUR][1000 genomes]
rs2460069	0.83[EUR][1000 genomes]
rs2462743	0.91[EUR][1000 genomes]
rs2462757	0.80[EUR][1000 genomes]
rs2462759	0.83[EUR][1000 genomes]
rs2462763	0.83[EUR][1000 genomes]
rs2511380	0.83[EUR][1000 genomes]
rs2511390	0.89[EUR][1000 genomes]
rs2511403	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs4415716	0.96[EUR][1000 genomes]
rs56355412	0.96[EUR][1000 genomes]
rs7107851	0.98[EUR][1000 genomes]
rs7127616	0.82[JPT][hapmap]
rs72964616	0.86[EUR][1000 genomes]
rs72964618	0.84[EUR][1000 genomes]
rs72964621	0.87[EUR][1000 genomes]
rs72964623	0.87[EUR][1000 genomes]
rs72964624	0.87[EUR][1000 genomes]
rs72964625	0.89[EUR][1000 genomes]
rs72964634	0.90[EUR][1000 genomes]
rs72964664	0.90[EUR][1000 genomes]
rs72964672	0.94[EUR][1000 genomes]
rs72964674	0.96[EUR][1000 genomes]
rs72964683	0.96[EUR][1000 genomes]
rs72964690	0.96[EUR][1000 genomes]
rs72964693	0.96[EUR][1000 genomes]
rs72966608	0.98[EUR][1000 genomes]
rs72966612	0.96[EUR][1000 genomes]
rs72966637	0.98[EUR][1000 genomes]
rs925005	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[EUR][1000 genomes]
rs959342	0.83[EUR][1000 genomes]
rs959343	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049467	chr11:93651025-93778717	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv898183	chr11:93725384-93906735	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv898184	chr11:93741612-93969726	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1914723	HEPHL1	cis	Artery Tibial	GTEx
rs1914723	CNKSR2	trans	parietal	SCAN
rs1914723	FAM76B	cis	cerebellum	SCAN
rs1914723	GPR83	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93755600-93760600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:93755800-93761200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:93758000-93760600	Weak transcription	Fetal Lung	lung
4	chr11:93758000-93760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:93759400-93760600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:93759400-93761400	Weak transcription	NH-A	brain
7	chr11:93760200-93761000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:93760400-93764000	Enhancers	HMEC	breast
9	chr11:93760400-93764000	Enhancers	NHEK	skin

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