Variant report

Variant	rs4555536
Chromosome Location	chr3:85857616-85857617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11127905	0.90[JPT][hapmap]
rs11711972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12494196	0.90[JPT][hapmap]
rs12494511	0.80[EUR][1000 genomes]
rs12636273	0.81[TSI][hapmap]
rs13068185	0.81[EUR][1000 genomes]
rs13085195	0.81[EUR][1000 genomes]
rs1375218	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1375219	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1448607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1448616	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1562626	0.84[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs17334733	0.90[JPT][hapmap]
rs1839171	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1839172	0.93[YRI][hapmap]
rs2029051	0.90[JPT][hapmap]
rs2029052	0.90[JPT][hapmap]
rs2029053	0.90[JPT][hapmap]
rs2044654	1.00[JPT][hapmap]
rs2324938	0.85[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2325036	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2325037	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2875529	0.94[ASN][1000 genomes]
rs3901898	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs3906942	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3930071	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs4129497	0.82[EUR][1000 genomes]
rs4234702	0.85[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs4302392	0.90[JPT][hapmap]
rs4302393	0.82[EUR][1000 genomes]
rs4302394	0.90[GIH][hapmap];0.91[MEX][hapmap]
rs4488844	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs4504176	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4555539	0.87[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs4618235	0.89[JPT][hapmap]
rs4688896	0.83[CEU][hapmap]
rs4856279	0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs4856606	0.80[CHB][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs6549053	0.95[CEU][hapmap]
rs6549054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6549055	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6787901	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs6796380	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs6796402	0.92[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs6799453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7429346	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7611409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7612371	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7621146	0.96[CEU][hapmap];0.87[CHB][hapmap]
rs7624423	0.90[JPT][hapmap]
rs7637221	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7638774	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7642281	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs7653470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9309992	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9309996	0.81[CEU][hapmap]
rs9681744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9820133	0.90[JPT][hapmap]
rs9820262	0.90[JPT][hapmap]
rs9836755	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9843797	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap]
rs9844720	0.89[JPT][hapmap]
rs9851502	0.81[CHB][hapmap]
rs9864042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9876664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9881886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010541	chr3:85505839-85870597	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536625	chr3:85505839-85870597	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv532629	chr3:85763873-86608579	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv877106	chr3:85814620-86006210	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv877107	chr3:85814620-86037162	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4555536	ZNF654	cis	parietal	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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