Variant report

Variant	rs471419
Chromosome Location	chr10:90508010-90508011
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1653842	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1653843	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs167333	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs170004	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1769690	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769691	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769692	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769697	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1769700	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs182493	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs186226	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs303453	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs303454	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs303456	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs303457	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs303464	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs303505	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs303506	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs303507	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs303508	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs303510	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs365847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs372589	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs376045	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs377257	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs378308	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs378425	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs385397	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs387970	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs388265	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs390414	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs391683	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs406102	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs407433	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs407922	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs408387	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs410033	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs412927	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs415996	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs416957	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs424371	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs426118	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs426836	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs427687	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs432950	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs434401	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs437261	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs441719	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs442607	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs450130	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs450794	0.87[EUR][1000 genomes]
rs454439	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs516083	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56390975	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs814642	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs866514	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1043015	chr10:90467067-90593692	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv467415	chr10:90478483-90600865	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv551840	chr10:90478483-90600865	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
9	nsv1052613	chr10:90500521-90526379	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs471419	LIPN	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90495600-90514000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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