Variant report

Variant	rs10749585
Chromosome Location	chr10:90199817-90199818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90195064..90196949-chr10:90198121..90201199,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10509544	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10736353	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[EUR][1000 genomes]
rs10736355	0.96[EUR][1000 genomes]
rs10788595	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10788597	1.00[CEU][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10788601	0.97[EUR][1000 genomes]
rs10788604	0.96[EUR][1000 genomes]
rs10887820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266064	1.00[CEU][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12778446	0.80[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes]
rs1426620	0.84[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1935580	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2153856	0.93[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2477957	0.82[JPT][hapmap]
rs6586130	0.95[EUR][1000 genomes]
rs7073799	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7077182	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7096710	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs7895199	0.92[EUR][1000 genomes]
rs7897033	0.80[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7907866	0.97[EUR][1000 genomes]
rs7913372	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7919420	0.97[EUR][1000 genomes]
rs7922053	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895879	chr10:90015725-90219298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	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
4	nsv1054984	chr10:90122512-90278038	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10749585	LIPM	cis	cerebellum	SCAN
rs10749585	BTAF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90193800-90227600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:90198600-90202200	Weak transcription	Adipose Nuclei	Adipose
3	chr10:90199600-90202200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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