Variant report

Variant	rs12631850
Chromosome Location	chr3:160883062-160883063
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	chr3:160880908..160883416-chr3:160895673..160897836,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1026572	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1037888	0.89[CEU][hapmap]
rs10513562	0.81[CEU][hapmap]
rs10936223	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936224	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12493960	0.88[EUR][1000 genomes]
rs12495310	0.88[AMR][1000 genomes]
rs13066683	0.85[EUR][1000 genomes]
rs13083229	0.88[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes]
rs13098884	0.81[CEU][hapmap]
rs1478568	0.89[TSI][hapmap]
rs1599374	0.96[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs1599376	0.88[EUR][1000 genomes]
rs1599378	0.92[EUR][1000 genomes]
rs1599379	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1599381	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1599383	0.85[EUR][1000 genomes]
rs1599386	0.85[EUR][1000 genomes]
rs1599389	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1599390	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1609688	0.91[EUR][1000 genomes]
rs1610158	0.93[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs2306061	0.89[CEU][hapmap]
rs2593812	0.80[CEU][hapmap]
rs336572	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs4290817	0.88[AMR][1000 genomes]
rs4342141	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs4414866	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4557202	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4560315	0.88[AMR][1000 genomes]
rs4616689	0.84[EUR][1000 genomes]
rs4618258	0.96[CEU][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4856714	0.88[AMR][1000 genomes]
rs4856767	0.86[AMR][1000 genomes]
rs5004752	0.81[CEU][hapmap]
rs55688744	0.88[AMR][1000 genomes]
rs6441354	0.96[CEU][hapmap];0.86[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs6765270	0.89[EUR][1000 genomes]
rs6768818	0.88[AMR][1000 genomes]
rs6774635	0.85[EUR][1000 genomes]
rs6778254	0.97[EUR][1000 genomes]
rs6783085	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6789244	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791213	0.84[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs6799130	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6806054	0.81[CEU][hapmap]
rs6809256	0.84[AMR][1000 genomes]
rs7614375	0.94[EUR][1000 genomes]
rs7617204	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7619011	0.85[EUR][1000 genomes]
rs7622047	0.88[CEU][hapmap]
rs7625363	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7627528	0.85[AMR][1000 genomes]
rs7630768	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7632423	0.81[CEU][hapmap]
rs7633857	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7636941	0.86[AMR][1000 genomes]
rs7637086	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7647285	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7650703	0.85[EUR][1000 genomes]
rs7651087	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7652267	0.88[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs778642	0.81[CEU][hapmap]
rs778643	0.81[CEU][hapmap]
rs778649	0.81[CEU][hapmap]
rs778653	0.81[CEU][hapmap]
rs778654	0.81[CEU][hapmap]
rs778657	0.81[CEU][hapmap]
rs796609	0.81[CEU][hapmap]
rs898680	0.89[CEU][hapmap]
rs898681	0.88[CEU][hapmap]
rs899275	0.84[AMR][1000 genomes]
rs9290065	0.92[CEU][hapmap]
rs9290069	0.92[CEU][hapmap];0.97[EUR][1000 genomes]
rs9809522	0.88[AMR][1000 genomes]
rs980975	0.89[CEU][hapmap]
rs980976	0.89[CEU][hapmap]
rs9811594	0.81[CEU][hapmap]
rs9815222	0.86[AMR][1000 genomes]
rs9820825	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs9834659	0.88[AMR][1000 genomes]
rs9847866	0.85[CEU][hapmap]
rs9848239	0.85[EUR][1000 genomes]
rs9860360	0.81[CEU][hapmap]
rs9864752	0.81[CEU][hapmap];0.90[AMR][1000 genomes]
rs9867582	0.90[EUR][1000 genomes]
rs9875200	0.81[CEU][hapmap]
rs9879687	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12631850	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs12631850	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160880800-160883200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:160881000-160886400	Weak transcription	Fetal Heart	heart
3	chr3:160881200-160884200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:160881800-160883200	ZNF genes & repeats	NHLF	lung
5	chr3:160882000-160883400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:160882000-160883400	ZNF genes & repeats	Osteobl	bone
7	chr3:160882400-160883200	Strong transcription	Ovary	ovary
8	chr3:160882400-160883200	ZNF genes & repeats	HSMM	muscle

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