Variant report

Variant	rs2029142
Chromosome Location	chr2:142801941-142801942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10179841	0.81[CHB][hapmap]
rs10190170	0.87[CHD][hapmap]
rs10496914	0.84[CHB][hapmap]
rs10803487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10928133	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10928134	0.88[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs11677754	0.91[ASN][1000 genomes]
rs11680286	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs11688838	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11691560	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs11691595	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs11692364	0.94[ASN][1000 genomes]
rs12105566	0.93[ASN][1000 genomes]
rs12105584	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs12470890	0.85[CHB][hapmap]
rs12618881	0.93[ASN][1000 genomes]
rs12619411	0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs12621782	0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12998297	0.94[ASN][1000 genomes]
rs13000270	0.84[ASN][1000 genomes]
rs13036224	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1349219	0.85[CHB][hapmap]
rs1349221	0.85[CHB][hapmap]
rs1375603	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1375606	0.81[CHB][hapmap]
rs1375609	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs1375612	0.83[CHB][hapmap]
rs1375613	0.81[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap]
rs1375616	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449475	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1449476	0.84[CHB][hapmap]
rs1449477	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap]
rs1449478	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap]
rs1449480	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs1449481	0.84[ASN][1000 genomes]
rs1449482	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1449489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1449490	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs1449494	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449495	1.00[ASN][1000 genomes]
rs1449496	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1449499	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1449501	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1449503	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs1449504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17824487	0.91[ASN][1000 genomes]
rs1868542	0.85[CHB][hapmap]
rs1868543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1868544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1900933	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1900934	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs2060592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167053	0.85[CHB][hapmap]
rs2197910	0.91[ASN][1000 genomes]
rs2218734	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2290140	0.83[MEX][hapmap]
rs2381203	0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap]
rs34392492	0.91[ASN][1000 genomes]
rs4550611	0.86[ASN][1000 genomes]
rs4662219	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs4662370	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]
rs4662373	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs62157626	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62157627	0.99[ASN][1000 genomes]
rs6744928	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs6754907	1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs736602	0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs7558803	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7566250	1.00[CHB][hapmap]
rs7581031	0.85[CHB][hapmap]
rs7598886	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7605112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7608258	0.85[CHB][hapmap]
rs7609479	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs957376	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap]
rs993935	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs9941495	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9941695	0.93[ASN][1000 genomes]
rs997123	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2029142	ZEB2	cis	cerebellum	SCAN
rs2029142	NXPH2	cis	cerebellum	SCAN
rs2029142	HNMT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142794400-142802400	Enhancers	NH-A	brain
2	chr2:142795800-142802600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:142796200-142809800	Weak transcription	Brain Substantia Nigra	brain
4	chr2:142800400-142803400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:142800400-142810200	Weak transcription	Brain Anterior Caudate	brain
6	chr2:142801200-142802600	Enhancers	Hela-S3	cervix
7	chr2:142801600-142802000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:142801800-142802200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:142801800-142802200	Enhancers	HMEC	breast
10	chr2:142801800-142803000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr2:142801800-142803000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr2:142801800-142803000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr2:142801800-142803400	Enhancers	HUES48 Cell Line	embryonic stem cell

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