Variant report

Variant	rs9879687
Chromosome Location	chr3:160874938-160874939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1026572	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs10936223	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936224	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12495310	0.88[AMR][1000 genomes]
rs12631850	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13083229	0.88[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs1478568	0.93[TSI][hapmap]
rs1599374	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1599378	0.82[EUR][1000 genomes]
rs1599379	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1599381	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1599389	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1599390	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1609688	0.81[EUR][1000 genomes]
rs16831830	0.81[CHB][hapmap]
rs336572	0.83[TSI][hapmap]
rs4290817	0.88[AMR][1000 genomes]
rs4557202	0.82[CEU][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs4560315	0.88[AMR][1000 genomes]
rs4618258	0.81[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4856714	0.88[AMR][1000 genomes]
rs4856767	0.86[AMR][1000 genomes]
rs55688744	0.88[AMR][1000 genomes]
rs6441354	0.82[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6768818	0.88[AMR][1000 genomes]
rs6778254	0.86[EUR][1000 genomes]
rs6783085	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6789244	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6791213	0.84[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes]
rs6799130	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6809256	0.84[AMR][1000 genomes]
rs7614375	0.83[EUR][1000 genomes]
rs7617204	0.83[EUR][1000 genomes]
rs7625363	0.83[EUR][1000 genomes]
rs7627528	0.85[AMR][1000 genomes]
rs7630674	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7630768	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7633857	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7636941	0.86[AMR][1000 genomes]
rs7637086	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7647285	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7651087	0.83[EUR][1000 genomes]
rs7652267	0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs899275	0.84[AMR][1000 genomes]
rs9290069	0.86[EUR][1000 genomes]
rs9809522	0.88[AMR][1000 genomes]
rs9815222	0.86[AMR][1000 genomes]
rs9834659	0.88[AMR][1000 genomes]
rs9864752	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9879687	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs9879687	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:5 , 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	chr3:160867400-160877800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:160867600-160880800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:160868400-160875800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links