Variant report

Variant	rs9819250
Chromosome Location	chr3:136795393-136795394
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136794352..136796925-chr3:136800790..136802653,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1023765	0.86[AMR][1000 genomes]
rs10935221	0.85[AMR][1000 genomes]
rs13098923	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1351892	0.84[AMR][1000 genomes]
rs1470143	0.86[AMR][1000 genomes]
rs1484787	0.86[AMR][1000 genomes]
rs1484794	0.84[AMR][1000 genomes]
rs361235	0.80[MEX][hapmap]
rs3899122	0.84[AMR][1000 genomes]
rs4678286	0.84[AMR][1000 genomes]
rs6439683	0.83[AMR][1000 genomes]
rs6439685	0.83[AMR][1000 genomes]
rs6439686	0.83[AMR][1000 genomes]
rs6773448	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781928	0.86[AMR][1000 genomes]
rs6795587	0.84[ASN][1000 genomes]
rs6806914	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807138	0.83[AMR][1000 genomes]
rs6808049	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808051	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627723	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646139	0.86[AMR][1000 genomes]
rs9289525	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969329	0.84[AMR][1000 genomes]
rs9810065	0.85[ASN][1000 genomes]
rs9818478	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9818918	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9822931	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826507	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838513	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9843104	0.85[AMR][1000 genomes]
rs9843219	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856620	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9870582	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9874836	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882135	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524856	chr3:136693459-137190765	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1012111	chr3:136695367-137343430	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9819250	TFDP2	cis	parietal	SCAN
rs9819250	SPSB4	cis	cerebellum	SCAN
rs9819250	GRK7	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136769400-136796200	Weak transcription	NHEK	skin
2	chr3:136782000-136804600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:136786200-136798000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:136795200-136800200	Weak transcription	Esophagus	oesophagus

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