Variant report

Variant	rs13085336
Chromosome Location	chr3:160880599-160880600
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160878230..160881032-chr4:153917101..153919182,2	MCF-7	breast:
2	chr3:160822678..160824356-chr3:160879261..160881379,2	MCF-7	breast:
3	chr3:160879167..160881201-chr3:160940682..160943022,2	K562	blood:

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10154889	0.85[CEU][hapmap]
rs11712713	0.82[EUR][1000 genomes]
rs11717272	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs11720263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11915989	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11922957	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11922959	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13059758	0.81[AMR][1000 genomes]
rs13060601	0.93[EUR][1000 genomes]
rs13071892	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13098896	0.84[EUR][1000 genomes]
rs13256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1562464	0.90[CEU][hapmap]
rs1599388	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16831886	0.94[EUR][1000 genomes]
rs28384382	0.86[AMR][1000 genomes]
rs34105342	0.91[AMR][1000 genomes]
rs34221255	0.82[EUR][1000 genomes]
rs34630898	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35127376	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35589595	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35914913	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4494975	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4521287	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4856700	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6441362	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6772723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6794882	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs68166680	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73021215	0.81[EUR][1000 genomes]
rs73023235	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7618924	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7624185	0.90[CEU][hapmap]
rs7638370	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs964533	0.90[CEU][hapmap]
rs9812507	0.90[CEU][hapmap]
rs9822435	0.90[CEU][hapmap];0.80[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];0.88[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13085336	SPTSSB	cis	Thyroid	GTEx
rs13085336	SPTSSB	cis	Adipose Subcutaneous	GTEx
rs13085336	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs13085336	SPTSSB	cis	Nerve Tibial	GTEx

Chromatin state (count:9 , 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	chr3:160867600-160880800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:160876200-160880600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:160879000-160880600	Weak transcription	HUVEC	blood vessel
6	chr3:160880000-160880600	Weak transcription	Fetal Heart	heart
7	chr3:160880200-160880600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:160880200-160881200	Enhancers	HMEC	breast
9	chr3:160880400-160881200	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links