Variant report

Variant	rs1580253
Chromosome Location	chr3:160767150-160767151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10513560	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10936216	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12496196	0.88[ASN][1000 genomes]
rs1447608	0.87[EUR][1000 genomes]
rs1447609	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1530636	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1562465	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1580254	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2121721	0.88[EUR][1000 genomes]
rs2889391	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34462546	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34884182	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35187206	0.86[AMR][1000 genomes]
rs6441345	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6441346	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6763532	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6769927	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6770180	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6774203	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6791375	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6808311	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6808386	0.85[EUR][1000 genomes]
rs7613316	0.85[EUR][1000 genomes]
rs7616249	0.87[EUR][1000 genomes]
rs7635796	0.85[EUR][1000 genomes]
rs7644586	0.86[EUR][1000 genomes]
rs898682	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9813700	0.87[EUR][1000 genomes]
rs9839984	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9840600	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846254	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857743	0.87[EUR][1000 genomes]
rs9858335	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9860182	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873705	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[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
rs1580253	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160745200-160782600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:160760800-160767600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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