Variant report

Variant	rs10845534
Chromosome Location	chr12:12570511-12570512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12568811..12571740-chr12:12581902..12583634,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10459099	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10505766	1.00[JPT][hapmap]
rs10743984	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10743986	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10743987	1.00[CHB][hapmap]
rs10772558	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10772560	0.82[AMR][1000 genomes]
rs10772561	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10772562	0.80[AMR][1000 genomes]
rs10772564	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10772565	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10845531	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10845535	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10845536	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10845538	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10845549	1.00[JPT][hapmap]
rs10845550	1.00[CHB][hapmap]
rs11054874	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap]
rs11054879	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11054885	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11054895	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11054898	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11054900	0.82[AMR][1000 genomes]
rs11054902	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11054904	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11054917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs11054918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs11531025	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11537452	0.89[ASN][1000 genomes]
rs11559836	0.82[AMR][1000 genomes]
rs12301872	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2111270	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2417186	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs918115	1.00[CHB][hapmap]
rs9645752	0.85[GIH][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10845534	LOH12CR1	cis	parietal	SCAN
rs10845534	KLRA1	cis	cerebellum	SCAN
rs10845534	LOH12CR1	cis	cerebellum	SCAN
rs10845534	ETV6	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
2	chr12:12557200-12572400	Weak transcription	Primary T cells from cord blood	blood
3	chr12:12558000-12586000	Weak transcription	Pancreas	Pancrea
4	chr12:12562400-12576200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:12565200-12585000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:12569000-12576800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr12:12569800-12570600	Enhancers	HepG2	liver
8	chr12:12570400-12571400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:12570400-12571800	Weak transcription	A549	lung

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