Variant report

Variant	rs12266064
Chromosome Location	chr10:90171971-90171972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10509544	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736353	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10736355	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10749585	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]
rs10788595	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10788597	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10788601	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10788604	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10788605	0.87[AMR][1000 genomes]
rs10887818	0.82[CHB][hapmap]
rs10887820	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]
rs10887827	0.87[AMR][1000 genomes]
rs10887829	0.95[MEX][hapmap];0.87[AMR][1000 genomes]
rs12778446	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1342451	0.82[CHB][hapmap]
rs1409134	0.95[MEX][hapmap];0.87[AMR][1000 genomes]
rs1426620	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1617881	0.81[CHB][hapmap]
rs1935580	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2153856	0.93[CEU][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6586130	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7077182	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7096710	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7895199	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7897033	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7902230	0.86[AMR][1000 genomes]
rs7907866	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7913372	1.00[CEU][hapmap];0.80[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7918921	0.82[CHB][hapmap]
rs7919420	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs792205	0.82[CHB][hapmap]
rs7922053	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs792230	0.82[CHB][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12266064	LIPM	cis	cerebellum	SCAN
rs12266064	BTAF1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90159800-90172800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:90168000-90172800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr10:90168400-90172600	Weak transcription	Primary B cells from cord blood	blood
4	chr10:90168400-90172800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr10:90169800-90173000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr10:90169800-90173200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr10:90170400-90172800	Enhancers	GM12878-XiMat	blood
8	chr10:90171400-90175800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr10:90171600-90172000	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr10:90171600-90172200	Enhancers	Primary B cells from peripheral blood	blood
11	chr10:90171800-90173000	Weak transcription	Dnd41	blood
12	chr10:90171800-90177000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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