Variant report

Variant	rs1599389
Chromosome Location	chr3:160836006-160836007
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	chr3:160835167..160838027-chr3:160903594..160905386,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1026572	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs1037888	0.92[CEU][hapmap]
rs10513559	0.85[CEU][hapmap]
rs10513562	0.85[CEU][hapmap]
rs10936223	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12493960	0.82[EUR][1000 genomes]
rs12631850	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12639128	0.84[CEU][hapmap]
rs13064176	0.85[CEU][hapmap]
rs13066683	0.91[EUR][1000 genomes]
rs13083229	0.87[TSI][hapmap]
rs13089559	0.84[CEU][hapmap]
rs13098884	0.85[CEU][hapmap]
rs1374793	0.83[CEU][hapmap]
rs1478568	0.87[TSI][hapmap]
rs1599374	0.92[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1599376	0.82[EUR][1000 genomes]
rs1599378	0.86[EUR][1000 genomes]
rs1599379	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1599381	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1599383	0.91[EUR][1000 genomes]
rs1599386	0.90[EUR][1000 genomes]
rs1599390	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1609688	0.85[EUR][1000 genomes]
rs1610158	0.96[CEU][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs17236725	0.85[CEU][hapmap]
rs17236746	0.85[CEU][hapmap]
rs17826438	0.88[CEU][hapmap]
rs2306061	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs2593812	0.84[CEU][hapmap]
rs4342141	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4414866	0.84[CEU][hapmap]
rs4557202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4616689	0.89[EUR][1000 genomes]
rs4618258	0.92[CEU][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4679922	0.85[CEU][hapmap]
rs4679924	0.81[CEU][hapmap]
rs4679926	0.87[CEU][hapmap]
rs5004752	0.85[CEU][hapmap]
rs6441354	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6764019	0.85[CEU][hapmap]
rs6765270	0.83[EUR][1000 genomes]
rs6774635	0.90[EUR][1000 genomes]
rs6778254	0.91[EUR][1000 genomes]
rs6783085	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6789244	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6791213	0.87[TSI][hapmap]
rs6799130	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6804650	0.85[CEU][hapmap]
rs6806054	0.85[CEU][hapmap]
rs7614375	1.00[EUR][1000 genomes]
rs7617204	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7619011	0.91[EUR][1000 genomes]
rs7622047	0.92[CEU][hapmap]
rs7625363	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7630674	0.81[CEU][hapmap]
rs7630768	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7632423	0.85[CEU][hapmap]
rs7633857	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7637086	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647285	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650703	0.90[EUR][1000 genomes]
rs7651087	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7652267	0.86[TSI][hapmap]
rs778642	0.85[CEU][hapmap]
rs778643	0.85[CEU][hapmap]
rs778649	0.85[CEU][hapmap]
rs778653	0.85[CEU][hapmap]
rs778654	0.85[CEU][hapmap]
rs778657	0.85[CEU][hapmap]
rs796609	0.85[CEU][hapmap]
rs898680	0.92[CEU][hapmap]
rs898681	0.92[CEU][hapmap]
rs9290065	0.96[CEU][hapmap]
rs9290069	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs980975	0.92[CEU][hapmap]
rs980976	0.92[CEU][hapmap]
rs9811594	0.85[CEU][hapmap]
rs9820825	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs9847866	0.89[CEU][hapmap]
rs9848239	0.90[EUR][1000 genomes]
rs9860360	0.85[CEU][hapmap]
rs9867582	0.96[EUR][1000 genomes]
rs9875200	0.85[CEU][hapmap]
rs9879687	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv877705	chr3:160818188-160836006	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877707	chr3:160820175-160836006	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1599389	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs1599389	PPM1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160835000-160836200	Enhancers	HUVEC	blood vessel

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