Variant report

Variant	rs4391525
Chromosome Location	chr9:17838833-17838834
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10120630	0.93[ASN][1000 genomes]
rs10122224	0.89[CEU][hapmap]
rs1049430	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs10756915	0.91[ASN][1000 genomes]
rs10756917	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10756918	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10810852	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10810853	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10810854	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10963281	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12555732	0.87[EUR][1000 genomes]
rs34504609	0.82[ASN][1000 genomes]
rs3736897	0.85[CEU][hapmap]
rs3808664	0.88[CEU][hapmap]
rs4265281	0.93[ASN][1000 genomes]
rs4284124	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4302936	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4373621	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4510955	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4523358	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4599896	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4961449	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4961450	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4961451	0.87[EUR][1000 genomes]
rs6475174	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6475177	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6475178	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6475181	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7018795	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7019050	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7025077	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7028412	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7029727	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7029798	0.92[CEU][hapmap]
rs7036989	0.81[CEU][hapmap]
rs7041618	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7857826	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7860861	0.89[CEU][hapmap]
rs7869721	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9298784	0.89[CEU][hapmap]
rs9406711	0.89[CEU][hapmap]
rs9407874	0.89[CEU][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	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
2	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
3	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
4	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
5	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
6	esv2761507	chr9:17810983-17901307	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4391525	SH3GL2	cis	cerebellum	SCAN
rs4391525	CNTLN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17838600-17843800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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