Variant report

Variant	rs4662370
Chromosome Location	chr2:142812609-142812610
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	chr2:142811783..142813457-chr2:142887329..142889786,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168702	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10179841	0.85[CHB][hapmap]
rs10190170	0.84[CHB][hapmap];0.84[CHD][hapmap];0.90[MEX][hapmap]
rs10193058	0.86[CEU][hapmap]
rs10803487	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs10928133	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10928134	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677754	0.98[ASN][1000 genomes]
rs11680286	0.95[CHB][hapmap];0.90[CHD][hapmap]
rs11688838	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11691560	0.87[CHD][hapmap]
rs11691595	0.87[CHD][hapmap]
rs11692364	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12105566	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12105584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618881	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619411	0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs12621782	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12998297	0.99[ASN][1000 genomes]
rs13000270	0.87[ASN][1000 genomes]
rs13036224	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1349222	0.81[ASN][1000 genomes]
rs1375603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1375606	0.85[CHB][hapmap]
rs1375609	0.87[CHD][hapmap]
rs1375613	0.83[CHD][hapmap]
rs1375616	0.93[ASN][1000 genomes]
rs1449475	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1449477	0.95[CHB][hapmap];0.92[CHD][hapmap]
rs1449478	0.95[CHB][hapmap];0.90[CHD][hapmap]
rs1449480	0.85[CHB][hapmap];0.87[CHD][hapmap];0.85[MEX][hapmap]
rs1449481	0.87[ASN][1000 genomes]
rs1449482	0.95[CHB][hapmap]
rs1449485	0.81[ASN][1000 genomes]
rs1449489	0.95[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs1449490	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs1449494	0.93[ASN][1000 genomes]
rs1449495	0.93[ASN][1000 genomes]
rs1449496	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1449498	0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs1449499	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1449501	0.88[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1449503	0.88[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1449504	0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs17824487	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1868543	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.91[ASN][1000 genomes]
rs1868544	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1900933	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1900934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029142	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs2060592	0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2197910	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2218734	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs2381203	0.83[CHD][hapmap]
rs34392492	0.98[ASN][1000 genomes]
rs4662219	0.87[CHD][hapmap]
rs4662373	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs62155598	0.81[ASN][1000 genomes]
rs62157626	0.92[ASN][1000 genomes]
rs62157627	0.92[ASN][1000 genomes]
rs6744928	0.87[CHD][hapmap]
rs6754907	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs736602	0.80[CHB][hapmap]
rs7558803	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7566250	0.95[CHB][hapmap]
rs7586417	0.80[CHB][hapmap]
rs7598886	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7605112	0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7609479	0.85[CHB][hapmap];0.87[CHD][hapmap];0.85[MEX][hapmap]
rs957376	0.95[CHB][hapmap];0.90[CHD][hapmap]
rs970600	0.81[MEX][hapmap]
rs993935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941495	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9941695	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997123	0.85[ASN][1000 genomes]

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	nsv530398	chr2:142474842-142843839	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv526107	chr2:142768518-142884248	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv875253	chr2:142805006-142855291	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4662370	NXPH2	cis	cerebellum	SCAN
rs4662370	ZEB2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142810800-142818200	Weak transcription	Brain Angular Gyrus	brain
2	chr2:142811600-142821400	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links