Variant report

Variant	rs9283525
Chromosome Location	chr2:213360073-213360074
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:213353950..213356217-chr2:213359072..213360969,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10153722	0.88[CEU][hapmap]
rs10168850	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10178298	0.83[CEU][hapmap]
rs10178687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190653	0.88[CEU][hapmap]
rs10194811	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10196652	0.88[CEU][hapmap]
rs10206719	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs10497976	0.82[CEU][hapmap]
rs11675580	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11689233	0.88[CEU][hapmap]
rs11892049	1.00[JPT][hapmap]
rs11894208	0.86[YRI][hapmap]
rs13015808	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13021394	1.00[JPT][hapmap]
rs13021610	1.00[JPT][hapmap]
rs13388843	0.87[CEU][hapmap]
rs13389790	1.00[CHB][hapmap]
rs13394464	0.88[CEU][hapmap]
rs1354617	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1384290	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1482381	0.88[CEU][hapmap]
rs1505372	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1586045	0.87[CEU][hapmap]
rs16848530	1.00[JPT][hapmap]
rs16848550	1.00[JPT][hapmap]
rs16848553	1.00[JPT][hapmap]
rs16848556	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16848564	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16848571	1.00[CHB][hapmap]
rs16848593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16848675	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16848707	0.84[CEU][hapmap]
rs16848787	0.84[CEU][hapmap]
rs17259208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17260933	0.88[CEU][hapmap]
rs17325381	0.87[CEU][hapmap]
rs17325821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17329875	1.00[JPT][hapmap]
rs1882352	0.88[CEU][hapmap]
rs1921630	0.88[CEU][hapmap]
rs1997470	0.88[CEU][hapmap]
rs2062930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2086612	0.88[CEU][hapmap]
rs2101151	0.86[CEU][hapmap]
rs2204853	0.88[CEU][hapmap]
rs4366846	0.82[EUR][1000 genomes]
rs55992489	0.83[ASN][1000 genomes]
rs6733009	0.82[CEU][hapmap]
rs6735807	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs6752299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs73063184	0.91[ASN][1000 genomes]
rs73063189	0.91[ASN][1000 genomes]
rs73067074	0.91[ASN][1000 genomes]
rs73079459	0.83[ASN][1000 genomes]
rs73079470	0.83[ASN][1000 genomes]
rs7568763	0.88[CEU][hapmap]
rs7569142	1.00[JPT][hapmap]
rs972488	0.88[CEU][hapmap]
rs972489	0.88[CEU][hapmap]
rs9808433	0.81[CEU][hapmap]
rs985995	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs999946	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004573	chr2:213186537-213365252	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
2	nsv432024	chr2:213314899-213446726	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv948878	chr2:213345197-213534298	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1008463	chr2:213356335-213388695	Enhancers ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9283525	MAP2	cis	cerebellum	SCAN
rs9283525	IKZF2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213353400-213362200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:213359800-213360600	Enhancers	Fetal Kidney	kidney
3	chr2:213359800-213361400	Enhancers	Fetal Heart	heart

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