Variant report

Variant	rs4873439
Chromosome Location	chr8:51161232-51161233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 185 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:182)

rs_ID	r²[population]
rs10092399	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs10093604	0.83[CEU][hapmap]
rs10094935	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10103047	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs10108468	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10109835	0.94[CEU][hapmap];0.91[CHB][hapmap]
rs10113812	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs10504098	0.86[ASW][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes]
rs10504099	0.93[CHB][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10808817	0.85[CHB][hapmap]
rs10957813	0.83[AMR][1000 genomes]
rs10957814	0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs10957853	0.92[CHB][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1117213	0.92[JPT][hapmap]
rs1160764	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1160795	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11775978	0.83[AMR][1000 genomes]
rs11778998	0.82[AMR][1000 genomes]
rs11780070	0.84[AMR][1000 genomes]
rs11781981	0.85[AMR][1000 genomes]
rs11784464	0.85[ASN][1000 genomes]
rs11784719	0.85[CHB][hapmap]
rs11786703	0.85[AMR][1000 genomes]
rs11986160	0.90[MEX][hapmap]
rs11991940	0.82[AMR][1000 genomes]
rs12056425	0.93[CHB][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12056426	0.93[CHB][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12541772	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12544631	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12545003	0.83[JPT][hapmap]
rs12545365	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12545915	0.93[CHB][hapmap];0.85[CHD][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12545927	0.84[CHB][hapmap]
rs12548940	0.88[CEU][hapmap]
rs12677522	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12677964	0.91[CHB][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12678703	0.87[ASN][1000 genomes]
rs12679317	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12679356	0.83[CEU][hapmap];0.93[CHB][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12680748	0.85[CHB][hapmap]
rs13248969	0.82[CHB][hapmap]
rs13249415	0.85[CHB][hapmap]
rs13251587	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13251725	0.82[CHB][hapmap]
rs13252320	0.92[CHB][hapmap]
rs13253758	0.85[CHB][hapmap]
rs13257851	0.83[JPT][hapmap]
rs13260021	0.82[CHB][hapmap]
rs13260265	0.83[CHD][hapmap];0.90[MEX][hapmap]
rs13260288	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs13275607	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs13277538	0.84[AMR][1000 genomes]
rs13282956	0.92[CHB][hapmap]
rs1349316	0.81[CEU][hapmap];0.93[CHB][hapmap]
rs1349317	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1375944	0.91[JPT][hapmap]
rs1375945	0.85[CHB][hapmap]
rs1375948	0.85[CHB][hapmap]
rs1380789	0.85[CHB][hapmap]
rs1380791	0.85[CHB][hapmap]
rs1380792	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs1450124	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs1450127	0.84[EUR][1000 genomes]
rs1450132	0.85[CHB][hapmap]
rs1450135	0.81[CHD][hapmap]
rs1460437	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1481471	0.83[JPT][hapmap]
rs1597426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs1597428	0.93[CHB][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1597429	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1597430	0.93[CHB][hapmap];0.92[CHD][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1597431	0.93[CHB][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1597432	0.92[JPT][hapmap]
rs1597433	0.92[JPT][hapmap]
rs16914346	0.90[MEX][hapmap]
rs16914376	0.84[AMR][1000 genomes]
rs16914459	0.85[AMR][1000 genomes]
rs16914780	0.83[JPT][hapmap]
rs17770910	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1824462	0.85[CHB][hapmap]
rs1868639	0.85[CHB][hapmap]
rs1901050	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1901055	0.93[CHB][hapmap]
rs1901056	0.85[CHB][hapmap]
rs1947254	0.92[JPT][hapmap]
rs203612	0.82[MEX][hapmap]
rs203632	0.82[MEX][hapmap]
rs203908	0.82[MEX][hapmap]
rs203930	0.82[MEX][hapmap]
rs203932	0.82[MEX][hapmap]
rs203940	0.82[MEX][hapmap]
rs203953	0.83[JPT][hapmap]
rs2084590	0.83[EUR][1000 genomes]
rs2084591	0.83[EUR][1000 genomes]
rs2167157	0.85[CHB][hapmap]
rs2219574	1.00[JPT][hapmap]
rs28510664	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957598	0.92[JPT][hapmap]
rs34217744	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34651805	0.85[ASN][1000 genomes]
rs34722367	0.84[AMR][1000 genomes]
rs34788367	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34908431	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34997857	0.87[AMR][1000 genomes]
rs35516514	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35857674	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36006902	0.84[AMR][1000 genomes]
rs3922033	0.94[CEU][hapmap];1.00[TSI][hapmap]
rs4256602	0.92[JPT][hapmap]
rs4330704	0.85[CHB][hapmap]
rs4339654	0.92[JPT][hapmap]
rs4398931	0.93[CHB][hapmap]
rs4410921	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs4448283	0.83[EUR][1000 genomes]
rs4448284	0.93[CHB][hapmap];0.92[CHD][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4534138	0.92[JPT][hapmap]
rs4543555	0.93[CHB][hapmap]
rs4577969	0.93[CHB][hapmap]
rs4604450	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs4633068	0.93[CHB][hapmap]
rs4873126	0.85[AMR][1000 genomes]
rs4873127	0.85[AMR][1000 genomes]
rs4873128	0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs4873129	0.81[MEX][hapmap];0.83[AMR][1000 genomes]
rs4873131	0.82[EUR][1000 genomes]
rs4873132	0.83[EUR][1000 genomes]
rs4873133	0.83[EUR][1000 genomes]
rs4873134	0.83[EUR][1000 genomes]
rs4873135	0.83[EUR][1000 genomes]
rs4873141	0.80[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];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4873142	0.85[CHB][hapmap]
rs4873143	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4873412	0.83[AMR][1000 genomes]
rs4873413	0.84[AMR][1000 genomes]
rs4873414	0.83[AMR][1000 genomes]
rs4873415	0.85[AMR][1000 genomes]
rs4873416	0.84[AMR][1000 genomes]
rs4873418	0.84[AMR][1000 genomes]
rs4873419	0.82[AMR][1000 genomes]
rs4873420	0.82[AMR][1000 genomes]
rs4873421	0.82[AMR][1000 genomes]
rs4873426	0.82[EUR][1000 genomes]
rs4873427	0.83[EUR][1000 genomes]
rs4873428	0.83[EUR][1000 genomes]
rs4873438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4873442	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4873443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4873447	0.85[CHB][hapmap]
rs56007637	0.83[AMR][1000 genomes]
rs62516672	0.85[AMR][1000 genomes]
rs62516685	0.84[AMR][1000 genomes]
rs62516687	0.84[AMR][1000 genomes]
rs6981805	0.85[CHB][hapmap]
rs6983498	0.83[EUR][1000 genomes]
rs6988843	0.82[MEX][hapmap]
rs6999627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs7000325	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7002235	0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs7003725	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7005672	0.92[JPT][hapmap]
rs7010037	0.84[AMR][1000 genomes]
rs7015950	0.91[JPT][hapmap]
rs7016161	0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs7017642	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7018082	0.82[EUR][1000 genomes]
rs7464491	0.93[CHB][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7817040	0.82[EUR][1000 genomes]
rs7817638	0.82[EUR][1000 genomes]
rs7821189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7822550	0.85[ASN][1000 genomes]
rs7824938	0.84[AMR][1000 genomes]
rs7825053	0.84[AMR][1000 genomes]
rs7835849	0.82[EUR][1000 genomes]
rs7839253	0.92[JPT][hapmap]
rs870754	0.81[MEX][hapmap];0.86[AMR][1000 genomes]
rs884561	0.84[AMR][1000 genomes]
rs898520	0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs9298295	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[EUR][1000 genomes]
rs9643720	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs968945	0.85[CHB][hapmap]
rs968947	0.85[CHB][hapmap]
rs987356	0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv948436	chr8:51115028-51917504	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv524203	chr8:51161232-51188675	Active TSS Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4873439	C8orf22	cis	parietal	SCAN
rs4873439	SNTG1	cis	cerebellum	SCAN
rs4873439	RNGTT	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:51156800-51161400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:51160200-51167200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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