Variant report

Variant	rs1426620
Chromosome Location	chr10:90160598-90160599
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	chr10:89622921..89625081-chr10:90159029..90160699,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171862	Chromatin interaction
ENSG00000227268	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10509544	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10736353	0.87[EUR][1000 genomes]
rs10736355	0.86[EUR][1000 genomes]
rs10749585	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]
rs10788595	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10788597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10788601	0.87[EUR][1000 genomes]
rs10788604	0.85[EUR][1000 genomes]
rs10887818	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs10887820	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]
rs12266064	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]
rs12778446	0.87[EUR][1000 genomes]
rs1342451	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1617881	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs1935580	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4934403	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6586130	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6586132	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs7077182	0.85[EUR][1000 genomes]
rs7096710	0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs7895199	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7897033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7907866	0.87[EUR][1000 genomes]
rs7913372	0.89[EUR][1000 genomes]
rs7918921	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs7919420	0.87[EUR][1000 genomes]
rs792205	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7922053	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs792209	0.82[JPT][hapmap]
rs792230	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs792236	0.81[ASN][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	esv1796143	chr10:90156447-90168074	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1426620	BTAF1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90156000-90161600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:90159400-90164400	Weak transcription	Fetal Lung	lung
3	chr10:90159800-90172800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr10:90160400-90165000	Enhancers	Liver	Liver

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