Variant report

Variant	rs11915989
Chromosome Location	chr3:160902259-160902260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160899826..160902456-chr3:160906456..160909122,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10154889	0.85[CEU][hapmap]
rs11717272	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11720263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11922957	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11922959	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13059758	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13060601	0.90[EUR][1000 genomes]
rs13071892	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13085336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13098896	0.81[EUR][1000 genomes]
rs13256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs1599388	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16831886	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28384382	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34105342	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34630898	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35127376	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35589595	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35914913	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4494975	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4521287	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4856700	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441362	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794882	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs68166680	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73023235	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7610800	0.84[YRI][hapmap]
rs7618924	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7638370	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs964533	0.90[CEU][hapmap]
rs9812507	0.90[CEU][hapmap]
rs9822435	0.90[CEU][hapmap]
rs9832109	0.90[CEU][hapmap]
rs9862086	0.83[EUR][1000 genomes]
rs9876142	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs9880269	0.83[EUR][1000 genomes]
rs9883566	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11915989	SPTSSB	cis	Adipose Subcutaneous	GTEx
rs11915989	B3GALT3	cis	multi-tissue	Pritchard
rs11915989	SPTSSB	cis	Thyroid	GTEx
rs11915989	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs11915989	SPTSSB	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160902200-160903400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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