Variant report

Variant	rs4618258
Chromosome Location	chr3:160869129-160869130
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160816607..160819169-chr3:160869043..160871012,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1026572	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1037888	0.82[CEU][hapmap]
rs10936223	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10936224	0.89[AMR][1000 genomes]
rs12493960	0.81[EUR][1000 genomes]
rs12495310	0.83[AMR][1000 genomes]
rs12631850	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13066683	0.80[EUR][1000 genomes]
rs13083229	0.81[AMR][1000 genomes]
rs1599374	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1599376	0.81[EUR][1000 genomes]
rs1599378	0.85[EUR][1000 genomes]
rs1599379	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1599381	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1599383	0.80[EUR][1000 genomes]
rs1599389	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1599390	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1609688	0.84[EUR][1000 genomes]
rs1610158	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2306061	0.85[CEU][hapmap]
rs4290817	0.83[AMR][1000 genomes]
rs4342141	0.86[CEU][hapmap]
rs4414866	0.85[CEU][hapmap]
rs4557202	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs4560315	0.83[AMR][1000 genomes]
rs4679926	0.80[CEU][hapmap]
rs4856714	0.83[AMR][1000 genomes]
rs4856767	0.81[AMR][1000 genomes]
rs55688744	0.83[AMR][1000 genomes]
rs6441354	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6765270	0.82[EUR][1000 genomes]
rs6768818	0.83[AMR][1000 genomes]
rs6778254	0.89[EUR][1000 genomes]
rs6783085	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6789244	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6799130	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7614375	0.86[EUR][1000 genomes]
rs7617204	0.86[EUR][1000 genomes]
rs7619011	0.80[EUR][1000 genomes]
rs7622047	0.82[CEU][hapmap]
rs7625363	0.84[EUR][1000 genomes]
rs7627528	0.80[AMR][1000 genomes]
rs7630768	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7633857	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7636941	0.81[AMR][1000 genomes]
rs7637086	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7647285	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7651087	0.86[EUR][1000 genomes]
rs898680	0.82[CEU][hapmap]
rs898681	0.82[CEU][hapmap]
rs9290065	0.88[CEU][hapmap]
rs9290069	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs9809522	0.83[AMR][1000 genomes]
rs980975	0.82[CEU][hapmap]
rs980976	0.82[CEU][hapmap]
rs9815222	0.81[AMR][1000 genomes]
rs9820825	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs9834659	0.83[AMR][1000 genomes]
rs9847866	0.82[CEU][hapmap]
rs9864752	0.83[AMR][1000 genomes]
rs9867582	0.83[EUR][1000 genomes]
rs9879687	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4618258	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160850400-160882400	Weak transcription	Ovary	ovary
2	chr3:160862200-160882400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:160866600-160869800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:160867400-160877800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:160867600-160880800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:160868400-160875800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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