Variant report

Variant	rs2923062
Chromosome Location	chr8:51278916-51278917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 163 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs10086867	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10093604	0.93[JPT][hapmap]
rs10094935	1.00[JPT][hapmap]
rs10108468	0.81[CHD][hapmap]
rs10109835	0.88[JPT][hapmap]
rs10504098	0.93[JPT][hapmap]
rs10504099	1.00[JPT][hapmap]
rs10808817	1.00[JPT][hapmap]
rs10957813	0.93[JPT][hapmap]
rs10957814	0.93[JPT][hapmap]
rs10957828	0.93[JPT][hapmap]
rs10957853	1.00[JPT][hapmap]
rs1117213	0.87[ASW][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.98[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11778998	0.93[JPT][hapmap]
rs11784719	1.00[JPT][hapmap]
rs11991940	0.93[JPT][hapmap]
rs12056425	1.00[JPT][hapmap]
rs12056426	1.00[JPT][hapmap]
rs12542067	0.93[JPT][hapmap]
rs12544473	1.00[JPT][hapmap]
rs12544631	1.00[JPT][hapmap]
rs12545003	0.93[ASW][hapmap];0.80[CEU][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap]
rs12545915	1.00[JPT][hapmap]
rs12545927	0.93[JPT][hapmap]
rs12675994	0.84[ASN][1000 genomes]
rs12677964	0.92[JPT][hapmap]
rs12679356	0.92[JPT][hapmap]
rs12679464	0.96[ASN][1000 genomes]
rs12680748	1.00[JPT][hapmap]
rs12681918	0.81[ASN][1000 genomes]
rs13248969	1.00[JPT][hapmap]
rs13249415	1.00[JPT][hapmap]
rs13251587	1.00[JPT][hapmap]
rs13251725	1.00[JPT][hapmap]
rs13252320	1.00[JPT][hapmap]
rs13253758	1.00[JPT][hapmap]
rs13257851	0.80[CEU][hapmap]
rs13259996	0.84[ASN][1000 genomes]
rs13260021	1.00[JPT][hapmap]
rs13260288	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs13275607	0.92[JPT][hapmap]
rs13278343	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13282956	1.00[JPT][hapmap]
rs13340639	0.91[JPT][hapmap]
rs1349316	0.93[JPT][hapmap]
rs1349317	1.00[JPT][hapmap]
rs1375942	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375944	1.00[JPT][hapmap]
rs1375945	1.00[JPT][hapmap]
rs1375947	0.81[ASN][1000 genomes]
rs1375948	1.00[JPT][hapmap]
rs1380789	1.00[JPT][hapmap]
rs1380790	0.93[JPT][hapmap]
rs1380791	1.00[JPT][hapmap]
rs1380792	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs1450127	0.93[JPT][hapmap]
rs1450132	1.00[JPT][hapmap]
rs1450135	0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1450136	0.85[CEU][hapmap]
rs1481471	0.80[CEU][hapmap]
rs1597426	1.00[JPT][hapmap]
rs1597427	0.81[ASN][1000 genomes]
rs1597428	1.00[JPT][hapmap]
rs1597430	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs1597432	0.87[ASW][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.98[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1597433	0.92[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs16914780	0.92[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs16914781	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17770910	1.00[JPT][hapmap]
rs1824462	1.00[JPT][hapmap]
rs1868638	0.81[ASN][1000 genomes]
rs1868639	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1901055	1.00[JPT][hapmap]
rs1901056	1.00[JPT][hapmap]
rs1947254	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs2084590	0.93[JPT][hapmap]
rs2167157	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2385812	0.93[JPT][hapmap]
rs2923059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957598	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs2957600	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2957601	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[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35063719	0.84[ASN][1000 genomes]
rs4147344	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4242460	0.84[ASN][1000 genomes]
rs4256602	0.80[CEU][hapmap];0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs4292700	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4330704	1.00[JPT][hapmap]
rs4339654	0.93[ASW][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs4364645	0.93[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4398931	1.00[JPT][hapmap]
rs4410921	0.80[CEU][hapmap];0.91[CHB][hapmap];0.84[YRI][hapmap];0.84[ASN][1000 genomes]
rs4448284	1.00[JPT][hapmap]
rs4529480	0.93[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4534138	0.87[ASW][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.95[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4543555	1.00[JPT][hapmap]
rs4577969	0.93[JPT][hapmap]
rs4604450	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs4618709	0.81[ASN][1000 genomes]
rs4633068	1.00[JPT][hapmap]
rs4639524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4873128	0.93[JPT][hapmap]
rs4873129	0.93[JPT][hapmap]
rs4873132	0.85[JPT][hapmap]
rs4873133	0.93[JPT][hapmap]
rs4873134	0.93[JPT][hapmap]
rs4873135	0.93[JPT][hapmap]
rs4873137	0.93[JPT][hapmap]
rs4873142	1.00[JPT][hapmap]
rs4873413	0.93[JPT][hapmap]
rs4873415	0.93[JPT][hapmap]
rs4873417	0.93[JPT][hapmap]
rs4873418	0.93[JPT][hapmap]
rs4873419	0.93[JPT][hapmap]
rs4873420	0.93[JPT][hapmap]
rs4873428	0.93[JPT][hapmap]
rs4873431	0.93[JPT][hapmap]
rs4873433	0.93[JPT][hapmap]
rs4873442	1.00[JPT][hapmap]
rs4873447	1.00[JPT][hapmap]
rs4873451	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4873452	0.81[ASN][1000 genomes]
rs4873453	0.82[ASN][1000 genomes]
rs6473114	0.84[ASN][1000 genomes]
rs6981805	1.00[JPT][hapmap]
rs6983498	0.93[JPT][hapmap]
rs6986896	0.93[JPT][hapmap]
rs6989084	0.81[ASN][1000 genomes]
rs6990514	0.81[ASN][1000 genomes]
rs6991753	0.93[JPT][hapmap]
rs6994415	0.98[ASN][1000 genomes]
rs6995334	0.93[JPT][hapmap];0.89[YRI][hapmap]
rs6999627	1.00[JPT][hapmap]
rs6999722	0.86[JPT][hapmap]
rs7001686	0.93[JPT][hapmap]
rs7002235	0.93[JPT][hapmap]
rs7005672	0.92[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs7013247	0.86[JPT][hapmap]
rs7015950	0.93[ASW][hapmap];0.80[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs7016161	0.93[JPT][hapmap]
rs7017642	1.00[JPT][hapmap]
rs7018082	0.93[JPT][hapmap]
rs7464491	1.00[JPT][hapmap]
rs7816983	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7820992	0.80[CEU][hapmap]
rs7821189	1.00[JPT][hapmap]
rs7822367	0.81[ASN][1000 genomes]
rs7825063	0.93[JPT][hapmap]
rs7834452	0.81[ASN][1000 genomes]
rs7839253	0.93[ASW][hapmap];0.80[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.84[ASN][1000 genomes]
rs7845433	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs870754	0.93[JPT][hapmap]
rs884561	0.93[JPT][hapmap]
rs898520	0.93[JPT][hapmap]
rs968944	1.00[JPT][hapmap]
rs968945	1.00[JPT][hapmap]
rs968947	1.00[JPT][hapmap]
rs983055	0.93[JPT][hapmap]

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	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	nsv831312	chr8:51239772-51422844	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv525765	chr8:51269514-51284501	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
5	esv3369164	chr8:51278449-51280447	Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2923062	SNTG1	cis	cerebellum	SCAN
rs2923062	EFCAB1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:51276600-51289000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:51278800-51279000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum

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