Variant report

Variant	rs2576162
Chromosome Location	chr10:90319445-90319446
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	chr10:89620441..89622522-chr10:90319312..90321016,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10509547	0.90[CEU][hapmap]
rs10509548	0.90[CEU][hapmap];0.80[MEX][hapmap]
rs10509549	0.90[CEU][hapmap];0.80[MEX][hapmap]
rs10509550	0.90[CEU][hapmap]
rs10736359	0.95[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10736360	0.82[CEU][hapmap]
rs11816967	0.85[CEU][hapmap]
rs1325899	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1325901	0.86[CEU][hapmap]
rs1325904	0.95[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1342457	0.95[CEU][hapmap];0.80[MEX][hapmap]
rs1359581	0.94[CEU][hapmap];0.84[AMR][1000 genomes]
rs1359582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409133	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409136	0.82[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes]
rs1555839	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs1573074	0.90[CEU][hapmap]
rs17334741	0.86[ASW][hapmap];0.80[MEX][hapmap];0.87[AFR][1000 genomes]
rs17336288	0.90[CEU][hapmap]
rs17426488	0.90[CEU][hapmap]
rs1774977	0.86[ASW][hapmap];0.80[MEX][hapmap]
rs1980813	0.82[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes]
rs2437876	0.90[CEU][hapmap]
rs2477953	0.95[CEU][hapmap]
rs2477959	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576155	0.81[CEU][hapmap];0.88[AMR][1000 genomes]
rs2576158	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2576163	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576167	0.82[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2576173	0.95[CEU][hapmap]
rs2576177	0.95[CEU][hapmap]
rs2765451	0.88[CEU][hapmap]
rs2765453	1.00[CEU][hapmap]
rs2765457	0.95[CEU][hapmap];0.80[MEX][hapmap]
rs792201	0.86[CEU][hapmap];0.87[AFR][1000 genomes]
rs792202	0.87[AFR][1000 genomes]
rs792203	0.87[AFR][1000 genomes]
rs792231	0.86[ASW][hapmap];0.81[CEU][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes]
rs875050	0.82[CEU][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv533167	chr10:90236197-90341481	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv430254	chr10:90265420-90500520	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1044680	chr10:90316066-90466092	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv540740	chr10:90316066-90466092	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2576162	LIPA	cis	cerebellum	SCAN
rs2576162	FAS	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90312200-90342400	Weak transcription	Ovary	ovary
2	chr10:90315400-90322200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr10:90315400-90342400	Weak transcription	Aorta	Aorta
4	chr10:90317800-90341800	Weak transcription	Adipose Nuclei	Adipose
5	chr10:90318000-90320000	Weak transcription	NHLF	lung
6	chr10:90318400-90320200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr10:90318400-90320200	Weak transcription	Osteobl	bone
8	chr10:90319000-90321200	Enhancers	Hela-S3	cervix
9	chr10:90319200-90342000	Weak transcription	Pancreas	Pancrea
10	chr10:90319400-90320600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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