Variant report

Variant	rs4302936
Chromosome Location	chr9:17811161-17811162
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:33352554..33353197-chr9:17810608..17811353,2	MCF-7	breast:
2	chr9:17810623..17811776-chr9:18207859..18208526,4	MCF-7	breast:
3	chr9:17811052..17811931-chr9:18212974..18213863,4	MCF-7	breast:
4	chr9:17810712..17811652-chr9:18207926..18208828,3	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10120630	0.89[ASN][1000 genomes]
rs10122224	0.96[CEU][hapmap]
rs1049430	0.92[CEU][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10756912	0.87[AMR][1000 genomes]
rs10756915	0.88[ASN][1000 genomes]
rs10756917	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10756918	0.80[AMR][1000 genomes]
rs10810847	0.82[CEU][hapmap]
rs10810851	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs10810852	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10810853	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10810854	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10963281	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2182091	0.81[CEU][hapmap]
rs2209424	0.82[CEU][hapmap]
rs2209428	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs2209432	0.85[CEU][hapmap]
rs2224954	0.85[CEU][hapmap]
rs34504609	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3736897	0.92[CEU][hapmap];0.84[MEX][hapmap]
rs3808664	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs3808667	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs3808673	0.82[CEU][hapmap]
rs3808681	0.82[CEU][hapmap]
rs4265281	0.89[ASN][1000 genomes]
rs4284124	0.81[AMR][1000 genomes]
rs4302941	0.85[CEU][hapmap]
rs4373621	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4391525	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4510955	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4523358	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4599896	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4961449	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4961450	0.81[AMR][1000 genomes]
rs6475174	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6475177	0.81[AMR][1000 genomes]
rs6475178	0.81[AMR][1000 genomes]
rs6475181	0.82[AMR][1000 genomes]
rs7019050	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7025077	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7028412	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7029798	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs7032367	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7036989	0.88[CEU][hapmap]
rs7041618	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7857826	0.82[AMR][1000 genomes]
rs7860861	0.96[CEU][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes]
rs7869721	0.81[AMR][1000 genomes]
rs9298783	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs9298784	0.96[CEU][hapmap]
rs9406711	0.96[CEU][hapmap];0.87[MEX][hapmap]
rs9407874	0.96[CEU][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4302936	SH3GL2	cis	cerebellum	SCAN
rs4302936	CNTLN	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17796000-17812000	Weak transcription	Aorta	Aorta
2	chr9:17808400-17812000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:17810600-17811800	Enhancers	Hela-S3	cervix
4	chr9:17810600-17812600	Enhancers	Fetal Brain Male	brain
5	chr9:17810800-17811200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr9:17810800-17811200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr9:17810800-17811200	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr9:17810800-17811200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr9:17810800-17811200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:17810800-17811200	Enhancers	Fetal Brain Female	brain
11	chr9:17810800-17811200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr9:17810800-17812400	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr9:17811000-17812800	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links