Variant report

Variant	rs9407874
Chromosome Location	chr9:17788028-17788029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10122224	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1049430	0.88[CEU][hapmap]
rs10756912	0.85[AMR][1000 genomes]
rs10810851	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs2182091	0.82[MEX][hapmap]
rs2209428	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs2209432	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs2224954	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs3736897	0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3808664	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3808667	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs4302941	0.82[CEU][hapmap]
rs7029798	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7036989	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7860861	1.00[CEU][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9298783	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs9298784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9406711	0.83[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9407875	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv892675	chr9:17694823-17790526	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv613706	chr9:17718918-18090934	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv613707	chr9:17720175-18070475	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv613708	chr9:17720175-18072085	Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1034673	chr9:17739006-17916606	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1023089	chr9:17748811-17919574	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9407874	SH3GL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17784800-17799400	Weak transcription	Hela-S3	cervix
2	chr9:17787000-17800400	Weak transcription	Fetal Brain Female	brain
3	chr9:17787200-17791000	Weak transcription	Fetal Brain Male	brain
4	chr9:17787600-17788600	Enhancers	Pancreatic Islets	Pancreatic Islet

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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