Variant report

Variant	rs2244402
Chromosome Location	chr2:142085631-142085632
allele	A/G
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	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1033309	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1033311	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1121373	0.84[CEU][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap]
rs13398990	0.87[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap]
rs13406676	0.91[ASN][1000 genomes]
rs13406775	0.90[ASN][1000 genomes]
rs1357024	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1357025	0.87[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs1357026	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1357027	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1357028	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1357029	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1402473	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]
rs1402475	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1402476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1402477	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1521105	0.90[ASN][1000 genomes]
rs1521106	0.90[ASN][1000 genomes]
rs1521107	0.89[ASN][1000 genomes]
rs1521109	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1521110	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1521111	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1521112	0.88[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1533737	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1915491	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2049154	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2248431	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2248439	0.91[ASN][1000 genomes]
rs2683816	0.87[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2683818	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2683819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2683821	0.90[ASN][1000 genomes]
rs2683822	0.88[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs2683824	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs2683825	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2683827	0.84[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs2683828	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2683831	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2683832	0.84[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap]
rs2683833	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2683834	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2683838	0.91[ASN][1000 genomes]
rs2683839	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2683840	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2683841	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2683842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2683844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2683848	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2683849	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2683850	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2683851	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2683852	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2683853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2683854	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2683855	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2683856	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2683857	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2683858	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap]
rs2683860	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2683861	0.87[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2683862	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2683863	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2683864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714173	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2714174	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2714176	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2714177	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap]
rs2714180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714182	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714183	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714184	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714186	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714187	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714189	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714190	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714192	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714193	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714194	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2714195	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2714196	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714197	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714198	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714199	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714207	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2714208	0.84[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs2714212	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs2714214	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs2714217	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap]
rs2714219	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2714223	0.85[ASN][1000 genomes]
rs2714224	0.91[ASN][1000 genomes]
rs2714225	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2714226	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2714227	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2714228	0.88[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2714229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2714230	0.87[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap]
rs3107479	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3107480	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs3107481	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs3109348	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3109350	0.87[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs3109351	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3109352	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34784852	0.94[ASN][1000 genomes]
rs4245854	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4536594	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4622648	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4954895	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap]
rs4954897	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs4954898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs4954901	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4954902	0.88[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs57189720	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6757846	0.87[CEU][hapmap];0.84[CHB][hapmap];0.93[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
rs2244402	NXPH2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142084800-142086800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:142085200-142088600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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