Variant report

Variant	rs4237559
Chromosome Location	chr11:93309447-93309448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10765617	0.86[EUR][1000 genomes]
rs1080367	0.80[CEU][hapmap]
rs10831062	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10831063	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10831064	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10831076	0.89[EUR][1000 genomes]
rs10831077	0.89[EUR][1000 genomes]
rs10831079	0.87[EUR][1000 genomes]
rs11020421	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11020426	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11020427	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11020450	0.87[EUR][1000 genomes]
rs11020452	0.87[EUR][1000 genomes]
rs11020453	0.87[EUR][1000 genomes]
rs11020454	0.86[EUR][1000 genomes]
rs11020455	0.88[EUR][1000 genomes]
rs11020479	0.80[CEU][hapmap]
rs11606802	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12222957	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1939568	0.81[CEU][hapmap]
rs1939570	0.87[EUR][1000 genomes]
rs1939571	0.87[EUR][1000 genomes]
rs1939572	0.87[EUR][1000 genomes]
rs1944108	0.80[CEU][hapmap]
rs1954783	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2155247	0.87[EUR][1000 genomes]
rs2186685	0.80[CEU][hapmap]
rs2399688	0.87[ASN][1000 genomes]
rs34679231	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4753089	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4753093	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4753094	0.87[EUR][1000 genomes]
rs4753480	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67011570	0.88[EUR][1000 genomes]
rs7119935	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7120590	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs948017	0.87[EUR][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	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4237559	SCARNA9	cis	cerebellum	SCAN
rs4237559	SCARNA9	cis	parietal	SCAN
rs4237559	MED17	cis	parietal	SCAN
rs4237559	FN5	cis	multi-tissue	Pritchard
rs4237559	ANKRD49	cis	parietal	SCAN
rs4237559	MED17	cis	cerebellum	SCAN
rs4237559	C11orf54	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93302200-93310400	Weak transcription	Psoas Muscle	Psoas
2	chr11:93305800-93310000	Weak transcription	Hela-S3	cervix
3	chr11:93306800-93309800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:93306800-93310400	Weak transcription	A549	lung
5	chr11:93309200-93309600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr11:93309400-93310400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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