Variant report

Variant	rs1402473
Chromosome Location	chr2:142098162-142098163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1003130	0.86[ASW][hapmap];0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1033309	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1033311	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1121373	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs13398990	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs13406676	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13406775	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1357024	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1357025	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1357026	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1357027	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1357028	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1357029	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1402475	1.00[ASW][hapmap];0.84[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1402476	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1402477	1.00[ASW][hapmap];0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1521105	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1521106	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1521107	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1521109	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521111	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521112	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533737	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1915491	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2049154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244402	0.93[ASW][hapmap];0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2248431	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248439	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683816	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2683818	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2683819	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2683821	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2683822	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs2683824	0.80[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap]
rs2683825	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs2683827	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2683828	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2683831	0.80[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2683832	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2683833	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2683834	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2683838	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683839	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2683841	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683842	0.82[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap]
rs2683844	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2683848	0.91[ASN][1000 genomes]
rs2683849	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2683850	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2683851	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2683852	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2683853	0.83[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2683854	1.00[ASW][hapmap];0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2683855	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2683856	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2683857	1.00[ASW][hapmap];0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2683858	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap]
rs2683860	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2683861	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683862	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683863	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2683864	0.86[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2714173	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2714174	0.84[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs2714176	0.92[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2714177	0.80[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap]
rs2714180	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2714182	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2714183	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2714184	0.91[ASN][1000 genomes]
rs2714185	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2714186	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2714187	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2714188	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2714189	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2714190	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2714191	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2714192	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2714193	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2714194	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2714195	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2714196	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2714197	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2714198	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2714199	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2714207	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2714208	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2714212	0.80[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap]
rs2714214	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs2714217	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs2714219	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2714223	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2714224	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714225	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714228	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714229	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap]
rs2714230	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs3107479	0.93[ASN][1000 genomes]
rs3107480	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3107481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs3109348	0.88[ASN][1000 genomes]
rs3109350	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34784852	0.90[ASN][1000 genomes]
rs4245854	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4536594	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4622648	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4954895	1.00[ASW][hapmap];0.83[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.92[YRI][hapmap]
rs4954897	1.00[ASW][hapmap];0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap]
rs4954898	0.86[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap]
rs4954901	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4954902	0.89[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs57189720	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6757846	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv583198	chr2:141510791-142150620	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1009434	chr2:141832339-142156180	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2830111	chr2:142047759-142164422	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3693337	chr2:142047759-142164422	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv875230	chr2:142055133-142119323	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
7	nsv583203	chr2:142055133-142378975	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2757835	chr2:142071391-142217569	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2759095	chr2:142071391-142245947	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1402473	NXPH2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142097400-142098200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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