Variant report

Variant	rs4961449
Chromosome Location	chr9:17815641-17815642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10120630	0.95[ASN][1000 genomes]
rs10122224	0.88[CEU][hapmap]
rs1049430	1.00[CEU][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10756912	0.85[AMR][1000 genomes]
rs10756915	0.94[ASN][1000 genomes]
rs10756917	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10756918	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10810851	0.82[MEX][hapmap]
rs10810852	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10810853	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10810854	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10963281	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12555732	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2209428	0.82[MEX][hapmap]
rs2296367	0.82[CEU][hapmap]
rs34504609	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3736897	0.84[CEU][hapmap];0.84[MEX][hapmap]
rs3808664	0.88[CEU][hapmap]
rs3808667	0.82[MEX][hapmap]
rs3808675	0.82[CEU][hapmap]
rs4265281	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4284124	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4302936	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4373621	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4391525	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4510955	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4523358	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4599896	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4961450	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4961451	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6475174	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6475177	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6475178	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6475181	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7018795	0.83[EUR][1000 genomes]
rs7019050	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025077	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7028412	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7029727	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7029798	0.87[CEU][hapmap]
rs7032367	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7036989	0.96[CEU][hapmap]
rs7041618	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7857826	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7860861	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs7869721	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9298783	0.82[MEX][hapmap]
rs9298784	0.88[CEU][hapmap]
rs9406711	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs9407874	0.88[CEU][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv824867	chr9:17810486-17828870	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv8422	chr9:17810758-17829560	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	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
9	esv2757321	chr9:17811584-17828437	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv2759675	chr9:17811584-17828437	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv2754695	chr9:17811600-17828400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4961449	SH3GL2	cis	cerebellum	SCAN
rs4961449	CNTLN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17812400-17816200	Weak transcription	Fetal Heart	heart
2	chr9:17812600-17815800	Weak transcription	Fetal Brain Male	brain
3	chr9:17812800-17816400	Weak transcription	Fetal Brain Female	brain
4	chr9:17814600-17816400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links