Variant report

Variant	rs6441362
Chromosome Location	chr3:160877613-160877614
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	chr3:160876047..160878704-chr3:160883637..160886578,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10154889	0.85[CEU][hapmap]
rs11712713	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11717272	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11720263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11915989	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11922957	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11922959	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13060601	0.93[EUR][1000 genomes]
rs13071892	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13085336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13098896	0.85[EUR][1000 genomes]
rs13256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1562464	0.90[CEU][hapmap]
rs1599388	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16831886	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28384382	0.85[AMR][1000 genomes]
rs34105342	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34221255	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34630898	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35127376	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35589595	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35914913	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4494975	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4521287	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4856700	0.90[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6772723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6794882	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs68166680	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73021215	0.82[EUR][1000 genomes]
rs73023235	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7618924	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7624185	0.90[CEU][hapmap]
rs7638370	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs964533	0.90[CEU][hapmap]
rs9812507	0.90[CEU][hapmap]
rs9822435	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs9832109	0.90[CEU][hapmap]
rs9862086	0.86[EUR][1000 genomes]
rs9876142	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes]
rs9880269	0.86[EUR][1000 genomes]
rs9883566	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[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
rs6441362	SPTSSB	cis	Nerve Tibial	GTEx
rs6441362	SPTSSB	cis	Thyroid	GTEx
rs6441362	B3GALT3	cis	multi-tissue	Pritchard
rs6441362	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs6441362	SPTSSB	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:6 , 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	chr3:160876200-160880600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:160877200-160880200	Weak transcription	HMEC	breast

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