Variant report

Variant	rs1325904
Chromosome Location	chr10:90280938-90280939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10509547	0.95[CEU][hapmap]
rs10509548	0.95[CEU][hapmap];0.80[MEX][hapmap]
rs10509549	0.95[CEU][hapmap];0.80[MEX][hapmap]
rs10509550	0.95[CEU][hapmap]
rs10736359	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11816967	0.90[CEU][hapmap]
rs1325899	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1325901	0.90[CEU][hapmap]
rs1342457	1.00[CEU][hapmap];0.80[MEX][hapmap]
rs1359581	0.94[CEU][hapmap]
rs1359582	0.95[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1409133	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1409136	1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs1555839	0.80[CEU][hapmap];1.00[MEX][hapmap]
rs1573074	0.95[CEU][hapmap]
rs17334741	0.82[CEU][hapmap];0.80[MEX][hapmap]
rs17336288	0.95[CEU][hapmap]
rs17426488	0.95[CEU][hapmap]
rs1774977	0.82[CEU][hapmap];0.80[MEX][hapmap]
rs1980813	1.00[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs2437876	0.95[CEU][hapmap]
rs2477953	1.00[CEU][hapmap]
rs2477959	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2576155	0.83[AMR][1000 genomes]
rs2576158	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2576162	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]
rs2576163	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2576167	1.00[MEX][hapmap];0.82[TSI][hapmap]
rs2576173	1.00[CEU][hapmap]
rs2576177	1.00[CEU][hapmap]
rs2765451	0.94[CEU][hapmap]
rs2765453	0.95[CEU][hapmap]
rs2765457	1.00[CEU][hapmap];0.80[MEX][hapmap]
rs792201	0.90[CEU][hapmap]
rs792231	0.86[CEU][hapmap];0.80[MEX][hapmap]
rs875050	1.00[MEX][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv825500	chr10:90221443-90302503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1325904	FAS	cis	parietal	SCAN
rs1325904	LIPA	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90275400-90281200	Weak transcription	Ovary	ovary
2	chr10:90279800-90284000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr10:90280000-90281600	Weak transcription	Aorta	Aorta
4	chr10:90280400-90281400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:90280400-90285200	Weak transcription	HMEC	breast

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