Variant report

Variant	rs1486096
Chromosome Location	chr1:72584184-72584185
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1026566	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs11209899	0.87[YRI][hapmap]
rs11209906	0.87[YRI][hapmap]
rs11209916	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11209920	0.85[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11209921	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11209928	0.82[CEU][hapmap]
rs11209933	0.82[CEU][hapmap]
rs1194269	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1194283	0.82[CEU][hapmap]
rs1194286	0.81[CEU][hapmap]
rs12131816	0.87[YRI][hapmap]
rs12132044	0.85[ASW][hapmap];0.87[YRI][hapmap]
rs12133604	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12141628	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12402629	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12409966	0.92[YRI][hapmap]
rs1352082	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1385912	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486084	0.93[YRI][hapmap]
rs1486091	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1486093	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1486094	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1564970	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1675356	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs1858600	0.82[CEU][hapmap]
rs2200484	0.87[YRI][hapmap]
rs2220253	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2422135	0.87[YRI][hapmap]
rs2422136	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2422137	0.96[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2630390	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2630392	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2630400	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630406	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2630431	0.84[CEU][hapmap]
rs2797540	0.82[CEU][hapmap]
rs2797543	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2821239	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2821246	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2821285	0.84[CEU][hapmap]
rs2821293	0.82[CEU][hapmap]
rs2821295	0.81[TSI][hapmap]
rs2821296	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs56301492	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57316908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6699731	0.81[TSI][hapmap]
rs727726	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7515320	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7517923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7541218	0.85[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7556006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1007073	chr1:72419858-72734657	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1006076	chr1:72477436-72700903	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv534996	chr1:72477436-72700903	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv428454	chr1:72504469-72926256	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv870851	chr1:72533927-72611715	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	nsv1013256	chr1:72541220-72620102	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
8	nsv461906	chr1:72549836-72683226	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
9	nsv461917	chr1:72549836-72683226	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
10	nsv546480	chr1:72549836-72683226	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
11	nsv870742	chr1:72552322-72611715	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
12	nsv461928	chr1:72555489-72683226	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
13	nsv546481	chr1:72555489-72683226	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
14	nsv461939	chr1:72555489-72717743	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv546482	chr1:72555489-72717743	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv546483	chr1:72581966-72659880	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
17	nsv997768	chr1:72583375-72665268	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1486096	NEGR1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72581800-72586800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:72583000-72584200	Enhancers	Colon Smooth Muscle	Colon
3	chr1:72583800-72585400	Weak transcription	HSMMtube	muscle

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