Variant report

Variant	rs170004
Chromosome Location	chr10:90463957-90463958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10509554	1.00[ASN][1000 genomes]
rs10736360	1.00[YRI][hapmap]
rs1169042	1.00[ASN][1000 genomes]
rs1214456	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1237989	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1325901	1.00[ASN][1000 genomes]
rs1359581	1.00[YRI][hapmap]
rs1409136	1.00[YRI][hapmap]
rs1653842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs167333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769682	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1769683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1769690	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769691	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769697	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769700	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182493	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186226	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980813	1.00[YRI][hapmap]
rs2231778	1.00[ASN][1000 genomes]
rs2576167	1.00[YRI][hapmap]
rs2765451	1.00[ASN][1000 genomes]
rs2901950	1.00[YRI][hapmap]
rs303453	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303454	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303456	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303457	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303464	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303467	1.00[ASN][1000 genomes]
rs303468	1.00[ASN][1000 genomes]
rs303474	1.00[ASN][1000 genomes]
rs303478	1.00[ASN][1000 genomes]
rs303479	1.00[ASN][1000 genomes]
rs303482	1.00[ASN][1000 genomes]
rs303483	1.00[ASN][1000 genomes]
rs303488	1.00[ASN][1000 genomes]
rs303489	1.00[ASN][1000 genomes]
rs303500	1.00[ASN][1000 genomes]
rs303502	1.00[ASN][1000 genomes]
rs303505	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303506	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303507	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303508	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303516	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303517	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303531	1.00[ASN][1000 genomes]
rs303532	1.00[ASN][1000 genomes]
rs303537	1.00[ASN][1000 genomes]
rs303541	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs365847	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367605	1.00[ASN][1000 genomes]
rs372589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs376045	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376261	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs377257	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378425	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858283	1.00[ASN][1000 genomes]
rs387970	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388265	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390414	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs391683	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399496	1.00[ASN][1000 genomes]
rs406102	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407922	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408387	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41284088	1.00[ASN][1000 genomes]
rs412927	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415996	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416957	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420381	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs420653	1.00[CEU][hapmap]
rs424371	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426110	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs426118	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426836	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs427687	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432950	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435742	1.00[ASN][1000 genomes]
rs437261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442545	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs442607	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs450130	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450794	0.85[EUR][1000 genomes]
rs451949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs454439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471419	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs516083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55713122	1.00[ASN][1000 genomes]
rs56390975	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852496	1.00[ASN][1000 genomes]
rs61852497	1.00[ASN][1000 genomes]
rs814617	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814619	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814630	1.00[ASN][1000 genomes]
rs814642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs845134	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs866514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875050	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv430254	chr10:90265420-90500520	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1044680	chr10:90316066-90466092	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv540740	chr10:90316066-90466092	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv831941	chr10:90410488-90587332	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs170004	LIPN	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90462200-90464000	Enhancers	Hela-S3	cervix
2	chr10:90463200-90468800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:90463400-90464200	Enhancers	A549	lung
4	chr10:90463400-90465000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:90463400-90465400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:90463400-90465600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr10:90463400-90466000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr10:90463400-90466600	Weak transcription	HSMM	muscle
9	chr10:90463400-90466600	Weak transcription	Osteobl	bone
10	chr10:90463400-90467200	Weak transcription	Stomach Mucosa	stomach
11	chr10:90463600-90465000	Weak transcription	HMEC	breast
12	chr10:90463600-90465600	Weak transcription	NHEK	skin
13	chr10:90463600-90466400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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