Variant report

Variant	rs2376476
Chromosome Location	chr3:160708806-160708807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10154889	0.86[ASN][1000 genomes]
rs10433352	0.84[ASN][1000 genomes]
rs10513560	0.85[EUR][1000 genomes]
rs10936215	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10936216	0.84[EUR][1000 genomes]
rs11713987	0.82[ASN][1000 genomes]
rs11715733	0.84[ASN][1000 genomes]
rs12690576	0.82[EUR][1000 genomes]
rs13062651	0.82[ASN][1000 genomes]
rs13098529	0.84[EUR][1000 genomes]
rs1374787	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1447608	0.80[EUR][1000 genomes]
rs1447609	0.84[EUR][1000 genomes]
rs1530636	0.84[EUR][1000 genomes]
rs1562465	0.84[EUR][1000 genomes]
rs1580254	0.89[EUR][1000 genomes]
rs16831796	0.82[ASN][1000 genomes]
rs1868109	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2014810	0.84[ASN][1000 genomes]
rs2121721	0.82[EUR][1000 genomes]
rs2376477	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2889391	0.84[EUR][1000 genomes]
rs34462546	0.84[EUR][1000 genomes]
rs34884182	0.89[EUR][1000 genomes]
rs4679928	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57145341	0.82[ASN][1000 genomes]
rs6441345	0.84[EUR][1000 genomes]
rs6441346	0.85[EUR][1000 genomes]
rs6763532	0.85[EUR][1000 genomes]
rs6769927	0.86[EUR][1000 genomes]
rs6770180	0.85[EUR][1000 genomes]
rs6774203	0.85[EUR][1000 genomes]
rs6791375	0.89[EUR][1000 genomes]
rs6806015	0.95[ASN][1000 genomes]
rs6808311	0.87[EUR][1000 genomes]
rs733948	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs745707	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7610432	0.86[ASN][1000 genomes]
rs7611005	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7616249	0.81[EUR][1000 genomes]
rs7618455	0.82[ASN][1000 genomes]
rs7628389	0.86[ASN][1000 genomes]
rs898677	0.84[ASN][1000 genomes]
rs956447	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs964533	0.83[ASN][1000 genomes]
rs9812507	0.94[ASN][1000 genomes]
rs9813700	0.80[EUR][1000 genomes]
rs9832109	0.95[ASN][1000 genomes]
rs9839984	0.88[EUR][1000 genomes]
rs9857743	0.80[EUR][1000 genomes]
rs9857855	0.85[ASN][1000 genomes]
rs9858335	0.89[EUR][1000 genomes]
rs9873705	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1007004	chr3:160695108-160718154	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2376476	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs2376476	PSMC1P7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160697200-160710600	Weak transcription	Left Ventricle	heart
2	chr3:160705000-160720000	Weak transcription	Gastric	stomach
3	chr3:160706000-160711200	Weak transcription	Right Atrium	heart
4	chr3:160706400-160716000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:160708200-160712000	Weak transcription	Placenta	Placenta
6	chr3:160708600-160709000	Enhancers	Stomach Smooth Muscle	stomach

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