Variant report

Variant	rs2197879
Chromosome Location	chr13:39245188-39245189
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:39243748..39246515-chr13:39262271..39264131,2	MCF-7	breast:
2	chr13:39244482..39246478-chr13:39258303..39260583,2	MCF-7	breast:
3	chr13:39244540..39245431-chr13:39489325..39490251,2	MCF-7	breast:
4	chr13:39244484..39245347-chr13:39337636..39338399,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11147723	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11147724	0.95[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs11147725	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17244358	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053848	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2122208	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2122211	0.93[ASW][hapmap]
rs2122212	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2442335	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2442339	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2442340	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2442341	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2442343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2442344	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442373	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442379	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496418	0.82[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2496419	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2496420	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2496425	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35378642	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4329795	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55860060	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55922882	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6563629	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331440	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7991701	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs895895	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs930659	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs930660	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9566354	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576589	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576590	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576591	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576592	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576595	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634754	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9788341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][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	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2197879	CCNA1	cis	parietal	SCAN
rs2197879	CSNK1A1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39244600-39245200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr13:39244600-39245600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr13:39244600-39245800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr13:39244800-39246200	Enhancers	Stomach Smooth Muscle	stomach

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