Variant report

Variant	rs12485456
Chromosome Location	chr3:157195091-157195092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:157181063..157183847-chr3:157192329..157195122,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11718199	0.95[CEU][hapmap]
rs11923106	0.96[CEU][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13318762	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350150	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378797	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1378802	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1456093	0.82[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1456094	0.96[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1456095	0.96[CEU][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1456112	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1456113	0.96[CEU][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1550651	0.95[CEU][hapmap];0.87[YRI][hapmap]
rs1840667	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1988267	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2034094	0.96[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2316349	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2840046	0.96[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4679800	0.82[ASW][hapmap];0.95[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4680373	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7626974	0.96[CEU][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7629184	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs920759	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs973207	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9809137	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs988758	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.95[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	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12485456	VEPH1	cis	cerebellum	SCAN
rs12485456	PTX3	cis	cerebellum	SCAN
rs12485456	ARL14	cis	parietal	SCAN
rs12485456	C3orf55	cis	cerebellum	SCAN
rs12485456	C3orf55	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157185600-157211400	Weak transcription	HSMM	muscle
2	chr3:157187600-157210600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:157188000-157203000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:157189400-157199400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:157193600-157195200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:157194000-157212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:157194400-157210200	Weak transcription	NH-A	brain
8	chr3:157194600-157195400	Strong transcription	HUVEC	blood vessel
9	chr3:157194600-157198200	Weak transcription	Osteobl	bone
10	chr3:157194600-157198400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:157194600-157217000	Weak transcription	Pancreas	Pancrea
12	chr3:157194800-157212000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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