Variant report

Variant	rs4494975
Chromosome Location	chr3:160866768-160866769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10154889	0.83[AMR][1000 genomes]
rs10433352	0.84[AMR][1000 genomes]
rs11712713	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715733	0.84[AMR][1000 genomes]
rs11717272	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11720263	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11915989	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11922957	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11922959	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12696112	0.80[AMR][1000 genomes]
rs12696113	0.80[AMR][1000 genomes]
rs13060601	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13060718	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13061088	0.81[ASN][1000 genomes]
rs13071892	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13085336	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13098896	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13256	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13315565	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1599388	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16831796	0.82[AMR][1000 genomes]
rs16831886	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2014810	0.84[AMR][1000 genomes]
rs34105342	0.82[AMR][1000 genomes]
rs34221255	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34630898	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35127376	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35589595	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35914913	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4521287	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4679929	0.81[AMR][1000 genomes]
rs4856700	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57145341	0.82[AMR][1000 genomes]
rs6441362	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6772723	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6794882	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6806015	0.89[AMR][1000 genomes]
rs68166680	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73021215	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73023235	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610432	0.84[AMR][1000 genomes]
rs7618924	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7624185	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7628389	0.83[AMR][1000 genomes]
rs7638370	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs898677	0.84[AMR][1000 genomes]
rs964533	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9812507	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9822435	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9832109	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9857855	0.84[AMR][1000 genomes]
rs9862086	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9876142	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9880269	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9883566	0.87[AMR][1000 genomes];0.91[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4494975	SPTSSB	cis	Adipose Subcutaneous	GTEx
rs4494975	SPTSSB	cis	Thyroid	GTEx
rs4494975	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 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	chr3:160866400-160867800	Enhancers	HMEC	breast
4	chr3:160866400-160868400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr3:160866400-160868600	Enhancers	Osteobl	bone
6	chr3:160866600-160867600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:160866600-160868200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:160866600-160868400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:160866600-160868400	Enhancers	NH-A	brain
10	chr3:160866600-160868400	Enhancers	NHDF-Ad	bronchial
11	chr3:160866600-160869800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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