Variant report

Variant	rs2324938
Chromosome Location	chr3:86014136-86014137
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10084716	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11715949	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12494511	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12636273	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12714642	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13068011	0.80[EUR][1000 genomes]
rs13068185	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13085195	0.88[EUR][1000 genomes]
rs1375218	0.83[CEU][hapmap]
rs1375219	0.87[ASW][hapmap];0.83[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs1448607	0.85[GIH][hapmap];0.82[TSI][hapmap]
rs1448616	0.87[ASW][hapmap];0.84[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs1562626	0.87[ASW][hapmap];0.88[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs2324937	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs2324939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2324973	0.92[AMR][1000 genomes]
rs2324981	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes]
rs2325005	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs3901898	0.87[ASW][hapmap];0.84[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs3906942	0.82[AMR][1000 genomes]
rs3930071	0.92[CEU][hapmap]
rs4129497	0.88[EUR][1000 genomes]
rs4234702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4302393	0.88[EUR][1000 genomes]
rs4302394	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4308293	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4364177	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4488844	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4555536	0.85[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs4555539	0.92[CEU][hapmap]
rs4688896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4856279	0.87[ASW][hapmap];0.84[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs4856606	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4856607	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56282418	0.89[EUR][1000 genomes]
rs6549063	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6762937	0.84[EUR][1000 genomes]
rs6769012	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6782553	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6787901	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6796380	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6796402	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs6798987	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6799453	0.85[GIH][hapmap];0.84[TSI][hapmap]
rs7426412	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7609709	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611409	0.85[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs7614073	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7620544	0.85[EUR][1000 genomes]
rs7621146	0.87[CEU][hapmap]
rs7623735	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7625223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7626873	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7630752	1.00[CEU][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes]
rs7632162	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7634560	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs7636206	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7637221	0.84[CEU][hapmap]
rs7640041	0.87[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7642281	0.92[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7648895	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7650420	0.87[AMR][1000 genomes]
rs9309992	0.83[CEU][hapmap]
rs9309996	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9310000	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9713674	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9810861	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9824085	0.92[CEU][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9829446	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9832847	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9841158	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9846878	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9850482	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9851502	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9864042	0.85[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs9866273	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs9875386	0.92[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9985228	0.87[EUR][1000 genomes]
rs9985441	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv877108	chr3:85870363-86037162	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv877110	chr3:85892098-86037162	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv877111	chr3:85892098-86044224	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
6	nsv470727	chr3:85917289-86044224	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
7	nsv590913	chr3:85917289-86044224	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
8	nsv877112	chr3:85964737-86083716	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2324938	ZNF654	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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