Variant report

Variant	rs17725673
Chromosome Location	chr7:33494290-33494291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10235388	0.85[ASN][1000 genomes]
rs10251775	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12155002	0.84[ASN][1000 genomes]
rs12530700	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12536596	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12536844	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.81[ASN][1000 genomes]
rs12537512	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs12538649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1419912	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs17724206	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17726934	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1978333	0.81[ASN][1000 genomes]
rs2392235	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2392242	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs28789535	0.84[ASN][1000 genomes]
rs3948651	0.85[ASN][1000 genomes]
rs4720119	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62451190	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62451222	0.88[ASN][1000 genomes]
rs62451225	0.88[ASN][1000 genomes]
rs6946608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9886232	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9886325	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016416	chr7:33241443-33559477	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv916660	chr7:33272493-33506384	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv830944	chr7:33389892-33549882	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv934287	chr7:33470390-33512880	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv933237	chr7:33470390-33574046	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17725673	BBS9	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33475400-33516000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:33492200-33495200	Enhancers	HepG2	liver
3	chr7:33493000-33495600	Weak transcription	Fetal Lung	lung
4	chr7:33493000-33496400	Weak transcription	NHLF	lung
5	chr7:33493000-33502800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:33493200-33498600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:33493200-33498600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:33493200-33498600	Weak transcription	Osteobl	bone

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