Variant report

Variant	rs2109526
Chromosome Location	chr7:33511742-33511743
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10232000	0.82[CHB][hapmap];0.88[MEX][hapmap]
rs11769528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13227256	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13438256	0.91[JPT][hapmap]
rs1419922	0.87[MEX][hapmap]
rs17170246	0.88[MEX][hapmap]
rs17170247	0.88[MEX][hapmap];1.00[YRI][hapmap]
rs17170253	0.88[MEX][hapmap]
rs17170269	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17170271	0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs2041417	0.82[CHB][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2392232	0.88[ASN][1000 genomes]
rs35822718	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779239	0.95[JPT][hapmap]
rs3823763	0.87[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs3884597	0.91[JPT][hapmap]
rs4604335	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4723289	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6944723	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs71532578	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs740888	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7798938	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs961679	0.87[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs9639675	0.87[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs9784973	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	nsv934287	chr7:33470390-33512880	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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
5	nsv933018	chr7:33506325-33707270	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv520794	chr7:33506906-33517523	Enhancers Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2109526	BBS9	cis	parietal	SCAN

Chromatin state (count:10 , 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	chr7:33510800-33533200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:33511000-33511800	Enhancers	HSMMtube	muscle
4	chr7:33511000-33512400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:33511000-33512400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:33511000-33512600	Enhancers	Osteobl	bone
7	chr7:33511200-33512400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:33511200-33512600	Enhancers	Adipose Nuclei	Adipose
9	chr7:33511200-33512800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:33511600-33512000	Enhancers	Muscle Satellite Cultured Cells	--

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