Variant report

Variant	rs13099811
Chromosome Location	chr3:60753662-60753663
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	chr3:60746660..60748176-chr3:60753528..60755409,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11130781	0.87[ASN][1000 genomes]
rs11130782	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710207	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12185984	0.89[ASN][1000 genomes]
rs13059280	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065371	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067083	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs13073028	0.87[CHB][hapmap];0.96[CHD][hapmap];0.83[TSI][hapmap]
rs13098348	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098545	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569346	0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2064012	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs2142294	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2205342	0.94[CHB][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2205343	1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205344	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364293	0.82[ASN][1000 genomes]
rs2594170	0.82[ASN][1000 genomes]
rs2594171	0.82[ASN][1000 genomes]
rs2736731	0.82[ASN][1000 genomes]
rs4974227	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4974230	0.83[CHB][hapmap]
rs57203484	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57595293	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762120	0.82[ASN][1000 genomes]
rs6762122	0.81[ASN][1000 genomes]
rs6764320	0.82[ASN][1000 genomes]
rs6771383	0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6786213	0.93[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs6787897	0.90[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs7429680	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs926139	0.83[ASN][1000 genomes]
rs9754707	0.82[ASN][1000 genomes]
rs9823013	0.82[CHB][hapmap]
rs9840977	0.98[ASN][1000 genomes]
rs9842407	0.89[ASN][1000 genomes]
rs9847131	0.89[ASN][1000 genomes]
rs9878766	0.83[CHB][hapmap]
rs9878801	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs9881274	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs9882068	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv998815	chr3:60495872-60830769	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv999828	chr3:60537384-60785274	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13099811	APPL1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60746200-60756200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:60747200-60756000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:60747200-60756400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:60752000-60754200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:60753400-60754600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:60753600-60753800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr3:60753600-60754000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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