Variant report

Variant	rs6433602
Chromosome Location	chr2:177519429-177519430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:177509574..177513874-chr2:177513908..177519452,7	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10179687	0.95[EUR][1000 genomes]
rs10199487	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10202251	0.80[ASN][1000 genomes]
rs10210519	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1054978	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11695305	0.80[ASN][1000 genomes]
rs12467496	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12616772	0.81[ASN][1000 genomes]
rs12617412	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12693096	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs13019019	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13395810	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13428659	0.81[ASN][1000 genomes]
rs1448519	0.80[ASN][1000 genomes]
rs1448531	1.00[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs1562608	0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1562611	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16864180	0.81[ASN][1000 genomes]
rs17411687	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17610485	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1868340	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1975589	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2362866	0.80[ASN][1000 genomes]
rs2594950	0.90[JPT][hapmap]
rs2710024	0.81[ASN][1000 genomes]
rs34664243	0.84[EUR][1000 genomes]
rs35704455	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4893911	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4893912	0.96[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4893914	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4894189	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4894190	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4894191	0.80[ASN][1000 genomes]
rs6718739	0.81[ASN][1000 genomes]
rs6740315	0.82[ASN][1000 genomes]
rs6753693	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6760357	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72930221	0.80[ASN][1000 genomes]
rs7585434	0.96[EUR][1000 genomes];1.00[ASN][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	nsv834464	chr2:177375743-177534410	Bivalent Enhancer Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6433602	SP9	cis	parietal	SCAN
rs6433602	SP9	cis	cerebellum	SCAN
rs6433602	OSBPL6	cis	cerebellum	SCAN
rs6433602	KIAA1715	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:177516200-177536400	Weak transcription	Ovary	ovary
2	chr2:177517200-177521800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:177518200-177519600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr2:177518200-177519600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:177519000-177522200	Weak transcription	Fetal Kidney	kidney
6	chr2:177519200-177519600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
7	chr2:177519400-177521800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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