Variant report

Variant	rs4302394
Chromosome Location	chr3:85977701-85977702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10084716	1.00[CEU][hapmap];0.93[CHB][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11715949	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494511	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12636273	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12714642	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13068185	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13085195	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1375219	0.90[GIH][hapmap];0.95[MEX][hapmap]
rs1448607	0.90[GIH][hapmap]
rs1448616	0.90[GIH][hapmap];0.95[MEX][hapmap]
rs1562626	0.83[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2324937	0.95[CEU][hapmap]
rs2324938	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2324939	0.96[CEU][hapmap]
rs2324973	0.86[AMR][1000 genomes]
rs2324981	0.96[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs2325005	0.96[CEU][hapmap]
rs3901898	0.81[CHB][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap]
rs3906942	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3930071	0.88[CEU][hapmap];0.94[CHB][hapmap]
rs4129497	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4234702	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs4302393	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4308293	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4364177	0.83[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4488844	0.87[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4555536	0.90[GIH][hapmap];0.91[MEX][hapmap]
rs4555539	0.91[CEU][hapmap];0.94[CHB][hapmap]
rs4688896	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs4856279	0.88[GIH][hapmap];0.91[MEX][hapmap]
rs4856606	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4856607	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56282418	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6549061	0.83[ASN][1000 genomes]
rs6549063	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6762937	0.83[EUR][1000 genomes]
rs6769012	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6782553	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6787901	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6796380	0.87[CEU][hapmap];0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6796402	0.87[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6798987	0.83[EUR][1000 genomes]
rs6799453	0.90[GIH][hapmap]
rs7426412	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7609709	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7611409	0.90[GIH][hapmap];0.91[MEX][hapmap]
rs7614073	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7620544	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7621146	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs7623735	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs7625223	0.96[CEU][hapmap]
rs7626873	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630752	0.96[CEU][hapmap];0.86[AMR][1000 genomes]
rs7632162	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7634560	0.95[CEU][hapmap]
rs7636206	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7640041	0.83[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7642281	0.87[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7648895	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650420	0.81[AMR][1000 genomes]
rs9309992	0.81[CHB][hapmap]
rs9309996	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9310000	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9713674	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9810861	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9824085	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs9824980	0.82[EUR][1000 genomes]
rs9829446	0.95[CEU][hapmap];0.88[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9832847	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9841158	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9843797	0.90[GIH][hapmap];0.91[MEX][hapmap]
rs9846878	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9850482	0.94[CEU][hapmap];0.91[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9851502	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9864042	0.82[ASW][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap]
rs9866273	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs9875386	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9985228	0.86[EUR][1000 genomes]
rs9985441	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
3	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
4	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
5	nsv877109	chr3:85892098-86006210	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
6	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
7	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
8	nsv460754	chr3:85917289-86006210	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv460755	chr3:85917289-86006210	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv590912	chr3:85917289-86006210	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
11	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
12	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
13	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
rs4302394	ZNF654	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85965200-85987000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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