Variant report

Variant	rs2867062
Chromosome Location	chr20:40790633-40790634
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:40782305..40784731-chr20:40788079..40790643,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1883377	0.83[CHD][hapmap]
rs1883378	0.96[CEU][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1984399	0.92[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs2143008	0.96[CEU][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2143632	0.80[CHD][hapmap]
rs2179336	0.96[CEU][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2206168	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2206169	0.96[CEU][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2223425	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2223718	0.83[CHD][hapmap]
rs2867061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140521	0.92[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs4331574	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4425144	0.96[CEU][hapmap];0.80[CHD][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4507153	0.96[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs6016705	0.80[CHD][hapmap]
rs6016710	0.80[CHD][hapmap]
rs6016716	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6016726	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs6030011	0.90[CHB][hapmap]
rs6030018	0.92[ASN][1000 genomes]
rs6030033	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6030036	0.83[CHD][hapmap]
rs6030056	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6030069	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6030070	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs6030071	0.92[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs6030076	0.92[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs6030081	0.82[EUR][1000 genomes]
rs6030082	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6030083	0.83[EUR][1000 genomes]
rs6030084	0.83[CEU][hapmap]
rs6030085	0.92[CEU][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs6030087	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs6030088	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6030089	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6030096	0.92[CEU][hapmap];0.80[CHD][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs6030100	0.81[CHB][hapmap]
rs6065450	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6065451	0.82[EUR][1000 genomes]
rs6072651	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6072672	0.84[CEU][hapmap];0.96[MEX][hapmap]
rs6093584	0.81[CHD][hapmap]
rs6102713	0.81[CHD][hapmap]
rs6124435	0.82[EUR][1000 genomes]
rs6130062	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs6130068	0.85[CHB][hapmap]
rs6130071	0.83[CHD][hapmap]
rs6130074	0.83[CHD][hapmap]
rs6130091	0.81[EUR][1000 genomes]
rs727336	0.92[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs727337	0.92[CEU][hapmap]
rs728373	0.92[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs728374	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs742290	0.83[CHD][hapmap]
rs742291	0.96[CEU][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs926647	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs932358	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs979634	0.96[CEU][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]

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	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2867062	KCNS1	cis	parietal	SCAN
rs2867062	RBPJL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40788600-40790800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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