Variant report

Variant	rs1449478
Chromosome Location	chr2:142827984-142827985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1001629	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1011862	0.80[ASN][1000 genomes]
rs10173643	0.85[ASN][1000 genomes]
rs10179841	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs10190170	0.90[CHD][hapmap]
rs10496914	0.85[CEU][hapmap];0.84[CHB][hapmap]
rs10803487	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs10928133	0.91[ASN][1000 genomes]
rs10928134	0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[ASN][1000 genomes]
rs11677754	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11680286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs11688838	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11691560	0.85[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs11691595	0.85[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs11692364	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12105566	0.91[ASN][1000 genomes]
rs12105584	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs12470890	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs12618881	0.91[ASN][1000 genomes]
rs12621782	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12988578	0.81[EUR][1000 genomes]
rs12998297	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13000270	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13036224	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1349219	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1349221	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1349222	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1375603	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs1375606	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs1375609	0.85[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs1375612	0.83[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs1375613	0.84[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap]
rs1375616	0.88[ASN][1000 genomes]
rs1449475	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1449476	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1449477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs1449480	0.81[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1449481	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1449482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1449485	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1449489	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1449490	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449494	0.88[ASN][1000 genomes]
rs1449495	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1449496	0.88[ASN][1000 genomes]
rs1449498	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1449499	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1449501	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1449503	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1449504	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17824487	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1868542	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1868543	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1868544	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1900933	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1900934	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs2029142	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2060592	1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2167053	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2197910	0.92[ASN][1000 genomes]
rs2218734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290140	0.85[CHD][hapmap];0.82[MEX][hapmap]
rs2381203	0.85[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs34392492	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4662219	0.81[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs4662370	0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[ASN][1000 genomes]
rs4662373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4662389	0.80[ASN][1000 genomes]
rs62155598	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62157626	0.87[ASN][1000 genomes]
rs62157627	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6744928	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs6754907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558803	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7566250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7581031	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7586417	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs7598886	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7605112	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7608258	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7609479	0.81[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs957376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs993935	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs9941495	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9941695	0.91[ASN][1000 genomes]
rs997123	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9973706	0.87[JPT][hapmap];0.83[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1449478	HNMT	cis	parietal	SCAN
rs1449478	ZEB2	cis	cerebellum	SCAN
rs1449478	NXPH2	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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