Variant report

Variant	rs1599381
Chromosome Location	chr3:160867680-160867681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1026572	0.94[EUR][1000 genomes]
rs10936223	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10936224	0.87[AMR][1000 genomes]
rs12493960	0.82[EUR][1000 genomes]
rs12495310	0.81[AMR][1000 genomes]
rs12631850	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13066683	0.91[EUR][1000 genomes]
rs1599374	0.82[EUR][1000 genomes]
rs1599376	0.82[EUR][1000 genomes]
rs1599378	0.86[EUR][1000 genomes]
rs1599379	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1599383	0.91[EUR][1000 genomes]
rs1599386	0.90[EUR][1000 genomes]
rs1599389	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1599390	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1609688	0.85[EUR][1000 genomes]
rs1610158	0.91[EUR][1000 genomes]
rs2306061	0.81[EUR][1000 genomes]
rs4290817	0.81[AMR][1000 genomes]
rs4342141	0.89[EUR][1000 genomes]
rs4557202	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4560315	0.81[AMR][1000 genomes]
rs4616689	0.89[EUR][1000 genomes]
rs4618258	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4856714	0.81[AMR][1000 genomes]
rs55688744	0.81[AMR][1000 genomes]
rs6441354	1.00[EUR][1000 genomes]
rs6765270	0.83[EUR][1000 genomes]
rs6768818	0.81[AMR][1000 genomes]
rs6774635	0.90[EUR][1000 genomes]
rs6778254	0.91[EUR][1000 genomes]
rs6783085	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6789244	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6799130	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7614375	1.00[EUR][1000 genomes]
rs7617204	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7619011	0.91[EUR][1000 genomes]
rs7625363	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7630768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633857	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7637086	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7647285	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7650703	0.90[EUR][1000 genomes]
rs7651087	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9290069	0.91[EUR][1000 genomes]
rs9809522	0.81[AMR][1000 genomes]
rs9820825	0.91[EUR][1000 genomes]
rs9834659	0.81[AMR][1000 genomes]
rs9848239	0.90[EUR][1000 genomes]
rs9864752	0.81[AMR][1000 genomes]
rs9867582	0.96[EUR][1000 genomes]
rs9879687	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[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
rs1599381	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 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	chr3:160866400-160867800	Enhancers	HMEC	breast
4	chr3:160866400-160868400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr3:160866400-160868600	Enhancers	Osteobl	bone
6	chr3:160866600-160868200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:160866600-160868400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:160866600-160868400	Enhancers	NH-A	brain
9	chr3:160866600-160868400	Enhancers	NHDF-Ad	bronchial
10	chr3:160866600-160869800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:160867000-160868200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:160867000-160868200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:160867000-160868400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:160867400-160868000	Enhancers	NHLF	lung
15	chr3:160867400-160877800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:160867600-160880800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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