Variant report

Variant	rs13325518
Chromosome Location	chr3:160750434-160750435
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160748979..160751725-chr3:160821249..160823513,2	MCF-7	breast:
2	chr3:160749654..160751759-chr3:160753566..160755069,2	MCF-7	breast:
3	chr3:160746924..160750622-chr3:160787755..160791172,3	MCF-7	breast:
4	chr3:160717602..160719198-chr3:160748866..160750938,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1045448	0.89[CEU][hapmap]
rs10513560	0.89[CHD][hapmap];0.93[JPT][hapmap]
rs11709802	0.85[JPT][hapmap]
rs11922296	1.00[CEU][hapmap]
rs12107243	0.89[CEU][hapmap]
rs12488621	0.85[CEU][hapmap]
rs12494133	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12496196	0.86[JPT][hapmap]
rs12498008	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12696110	0.85[GIH][hapmap]
rs13319969	0.89[CEU][hapmap]
rs1348976	1.00[CEU][hapmap]
rs1374786	0.81[ASN][1000 genomes]
rs1374789	1.00[CEU][hapmap]
rs1374790	1.00[CEU][hapmap]
rs1447615	1.00[CEU][hapmap]
rs1530635	0.81[ASN][1000 genomes]
rs1530636	0.89[CHD][hapmap];0.93[JPT][hapmap]
rs1562465	0.93[JPT][hapmap]
rs1562466	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1599382	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16831756	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16831757	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16831758	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16831868	0.89[CEU][hapmap]
rs1839018	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs1868104	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1868106	0.83[GIH][hapmap]
rs1903422	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1947686	0.89[CEU][hapmap]
rs1971240	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2028988	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2061580	0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2231252	0.89[CEU][hapmap]
rs2279106	0.89[CEU][hapmap]
rs4443220	0.89[CEU][hapmap]
rs4465984	0.84[CEU][hapmap]
rs4608736	0.81[ASN][1000 genomes]
rs4679927	0.81[ASN][1000 genomes]
rs57009978	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58189630	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59483687	0.87[ASN][1000 genomes]
rs60875417	0.90[ASN][1000 genomes]
rs62282273	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6441345	0.87[CHD][hapmap];0.93[JPT][hapmap]
rs6441353	0.89[CEU][hapmap]
rs6763532	0.85[JPT][hapmap]
rs6763838	0.85[CEU][hapmap]
rs6774203	0.87[CHD][hapmap];0.87[JPT][hapmap]
rs6787694	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6795977	0.89[CEU][hapmap]
rs6797498	0.86[JPT][hapmap]
rs6801330	1.00[CEU][hapmap]
rs73158255	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7429731	0.85[CEU][hapmap]
rs7610732	0.86[JPT][hapmap]
rs7630896	0.85[CEU][hapmap]
rs7649954	0.85[CEU][hapmap]
rs778644	0.81[ASN][1000 genomes]
rs778647	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs778650	1.00[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs778651	0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs778652	0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs778655	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs778656	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs778658	0.86[AMR][1000 genomes]
rs778661	0.86[AMR][1000 genomes]
rs778662	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs796610	0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs814092	0.81[ASN][1000 genomes]
rs898676	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs898678	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs898679	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs898683	0.85[CEU][hapmap]
rs898684	0.85[CEU][hapmap]
rs898685	0.84[CEU][hapmap]
rs9818081	0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9824308	0.85[CEU][hapmap]
rs9850546	0.92[ASN][1000 genomes]
rs9858335	0.87[CHD][hapmap]
rs9861850	0.89[CEU][hapmap]
rs9879296	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[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
rs13325518	B3GALNT1	cis	Artery Tibial	GTEx

Chromatin state (count:3 , 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	chr3:160749400-160753200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:160749800-160759000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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