Variant report

Variant	rs1562465
Chromosome Location	chr3:160701442-160701443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160701391..160703637-chr3:160711563..160713672,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10513560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709802	0.81[JPT][hapmap]
rs12496196	0.81[JPT][hapmap]
rs12498008	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs12690576	0.87[CEU][hapmap]
rs13325518	0.93[JPT][hapmap]
rs1374786	0.89[ASN][1000 genomes]
rs1374787	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs1447608	1.00[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1447609	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530635	0.89[ASN][1000 genomes]
rs1530636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562466	0.87[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1580253	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1580254	0.82[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs1599382	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs16831758	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs1868104	0.81[JPT][hapmap]
rs1868108	0.87[CEU][hapmap]
rs1868109	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs1971240	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2028988	0.81[JPT][hapmap]
rs2061580	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs2121721	1.00[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2376476	0.84[EUR][1000 genomes]
rs2376477	0.85[EUR][1000 genomes]
rs2889391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34462546	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34884182	0.84[AMR][1000 genomes]
rs4608736	0.87[ASN][1000 genomes]
rs4679927	0.89[ASN][1000 genomes]
rs4679928	0.84[EUR][1000 genomes]
rs58189630	0.88[ASN][1000 genomes]
rs6441345	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763532	0.88[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769927	0.85[AMR][1000 genomes]
rs6770180	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6787694	0.82[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs6791375	0.83[AMR][1000 genomes]
rs6797498	0.81[JPT][hapmap]
rs6798966	0.87[ASN][1000 genomes]
rs6808311	0.85[AMR][1000 genomes]
rs6808386	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs733948	0.87[CEU][hapmap]
rs7610732	0.81[JPT][hapmap]
rs7611005	0.83[EUR][1000 genomes]
rs7613316	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs7616249	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs7626904	0.85[EUR][1000 genomes]
rs7626985	0.86[EUR][1000 genomes]
rs7635796	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs7640874	1.00[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs7644586	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs778644	0.89[ASN][1000 genomes]
rs778647	0.83[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs778650	0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs778651	0.83[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs778652	0.82[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs778655	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs778656	0.89[ASN][1000 genomes]
rs778658	0.87[ASN][1000 genomes]
rs778661	0.86[ASN][1000 genomes]
rs778662	0.89[ASN][1000 genomes]
rs796610	0.82[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs814092	0.89[ASN][1000 genomes]
rs898676	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs898682	0.87[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs956447	0.87[CEU][hapmap]
rs9813700	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9818081	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs9839984	0.82[CEU][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes]
rs9840600	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9846254	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9857743	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9858335	0.82[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs9860182	0.95[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9873705	0.85[AMR][1000 genomes]
rs9881807	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	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
3	nsv1007004	chr3:160695108-160718154	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1562465	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160697000-160704000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:160697200-160710600	Weak transcription	Left Ventricle	heart
3	chr3:160699200-160701600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:160700000-160702000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:160700800-160701600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:160701200-160703400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:160701200-160703600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:160701200-160704000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:160701400-160701600	Enhancers	Placenta	Placenta

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