Variant report

Variant	rs1580254
Chromosome Location	chr3:160767278-160767279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10513560	0.84[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs10936216	0.85[AMR][1000 genomes]
rs12496196	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12690576	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs1374787	0.95[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs1447609	0.82[AMR][1000 genomes]
rs1447626	0.91[CEU][hapmap]
rs1530636	0.83[CEU][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs1562465	0.82[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs1580253	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1868108	0.95[CEU][hapmap]
rs1868109	0.95[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs2121721	0.80[TSI][hapmap]
rs2376476	0.89[EUR][1000 genomes]
rs2376477	0.90[EUR][1000 genomes]
rs2889391	0.85[AMR][1000 genomes]
rs34462546	0.80[AMR][1000 genomes]
rs34884182	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35187206	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4679928	0.89[EUR][1000 genomes]
rs6441345	0.81[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes]
rs6441346	0.85[AMR][1000 genomes]
rs6763532	0.85[JPT][hapmap];0.85[AMR][1000 genomes]
rs6769927	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6770180	0.85[AMR][1000 genomes]
rs6774203	0.81[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs6791375	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6808311	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs733948	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs7611005	0.88[EUR][1000 genomes]
rs778651	0.80[JPT][hapmap]
rs898682	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs956447	0.95[CEU][hapmap]
rs9839984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840600	0.80[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9846254	0.97[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9857743	0.82[CEU][hapmap]
rs9858335	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9860182	0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873705	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881807	0.95[CEU][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1580254	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs1580254	C3orf57	cis	parietal	SCAN
rs1580254	PPM1L	cis	cerebellum	SCAN

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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