Variant report

Variant	rs1552372
Chromosome Location	chr8:50773302-50773303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 233 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:232)

rs_ID	r²[population]
rs10086004	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10089399	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10090657	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10092384	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10107423	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10111730	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10112215	0.85[MEX][hapmap]
rs1038534	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10504092	0.96[EUR][1000 genomes]
rs10504093	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs1074385	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957620	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957679	0.88[ASN][1000 genomes]
rs10957682	0.88[ASN][1000 genomes]
rs10957739	0.85[MEX][hapmap]
rs1157932	0.86[CHB][hapmap]
rs11777957	0.86[CHB][hapmap]
rs11781675	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11782597	0.81[EUR][1000 genomes]
rs11783631	0.86[CHB][hapmap]
rs11785147	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11786939	1.00[ASN][1000 genomes]
rs11787050	0.88[ASN][1000 genomes]
rs11989680	0.81[EUR][1000 genomes]
rs11991730	0.81[EUR][1000 genomes]
rs11992716	0.81[EUR][1000 genomes]
rs12541363	0.84[CHB][hapmap]
rs12542041	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12542687	0.85[ASN][1000 genomes]
rs12545695	0.84[ASN][1000 genomes]
rs12547245	0.97[ASN][1000 genomes]
rs12550124	0.81[ASN][1000 genomes]
rs12677051	1.00[ASN][1000 genomes]
rs13251355	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13255117	1.00[ASN][1000 genomes]
rs13261298	1.00[ASN][1000 genomes]
rs13267366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352112	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352113	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1352117	0.91[CEU][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs1385974	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385975	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385976	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1385980	0.85[ASN][1000 genomes]
rs1385982	1.00[ASN][1000 genomes]
rs1486241	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486242	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486243	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486245	0.95[EUR][1000 genomes]
rs1486251	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486252	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486253	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486254	1.00[ASN][1000 genomes]
rs1486258	0.84[CHD][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs1486263	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1552371	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1552373	1.00[ASN][1000 genomes]
rs1552375	0.98[ASN][1000 genomes]
rs1552377	0.97[ASN][1000 genomes]
rs1552378	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1552379	0.84[ASN][1000 genomes]
rs1580468	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586364	0.88[ASN][1000 genomes]
rs1601569	1.00[ASN][1000 genomes]
rs167629	0.81[CEU][hapmap]
rs16912794	1.00[ASN][1000 genomes]
rs16913087	1.00[ASN][1000 genomes]
rs16913172	0.96[ASN][1000 genomes]
rs16913461	1.00[ASN][1000 genomes]
rs16913472	1.00[ASN][1000 genomes]
rs16913475	1.00[ASN][1000 genomes]
rs16913687	0.88[ASN][1000 genomes]
rs16914039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs170331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17674389	0.81[EUR][1000 genomes]
rs17674783	0.96[EUR][1000 genomes]
rs17747294	0.96[EUR][1000 genomes]
rs17747567	0.96[EUR][1000 genomes]
rs17747896	0.96[EUR][1000 genomes]
rs17747929	0.96[EUR][1000 genomes]
rs182646	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1906014	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1906015	0.94[ASN][1000 genomes]
rs1979535	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979536	0.82[EUR][1000 genomes]
rs1994344	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015043	0.85[MEX][hapmap]
rs2086888	0.83[MEX][hapmap]
rs2129162	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129164	1.00[ASN][1000 genomes]
rs2129165	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2170953	0.88[CHD][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs2200494	0.81[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs223081	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2247368	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2385544	0.96[EUR][1000 genomes]
rs2385545	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385546	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385547	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385548	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2385554	0.81[CHD][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs2385696	0.86[CHB][hapmap]
rs2449957	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2449958	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2449960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2450285	0.82[EUR][1000 genomes]
rs2450286	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2450287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2450288	0.83[EUR][1000 genomes]
rs2450290	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2450291	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2628417	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2630550	0.81[CEU][hapmap]
rs28869911	0.82[ASN][1000 genomes]
rs318850	0.84[ASN][1000 genomes]
rs318851	0.88[CHD][hapmap]
rs318853	0.88[CHD][hapmap]
rs318854	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs318858	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs318859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs318860	0.81[CEU][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs318861	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs318862	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs318864	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs318870	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs318871	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs318872	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs318873	0.91[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs318874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs318875	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs318877	0.81[CEU][hapmap]
rs318884	0.81[CEU][hapmap]
rs318885	0.81[CEU][hapmap];0.97[TSI][hapmap]
rs318888	0.81[CEU][hapmap]
rs318890	0.81[CEU][hapmap];0.97[TSI][hapmap]
rs318894	0.83[TSI][hapmap]
rs318902	0.83[TSI][hapmap]
rs318903	0.83[TSI][hapmap]
rs318910	0.83[TSI][hapmap]
rs365318	0.81[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs366526	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs380279	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs384406	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs391798	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs402156	0.82[EUR][1000 genomes]
rs406337	0.83[EUR][1000 genomes]
rs415276	0.91[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4242455	0.81[ASN][1000 genomes]
rs4242456	0.86[CHB][hapmap]
rs4339657	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs436688	0.83[EUR][1000 genomes]
rs4377975	0.95[EUR][1000 genomes]
rs4383988	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4389954	0.81[ASN][1000 genomes]
rs4457345	0.81[ASN][1000 genomes]
rs4584153	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4873113	1.00[ASN][1000 genomes]
rs4873114	1.00[ASN][1000 genomes]
rs4873116	1.00[ASN][1000 genomes]
rs4873118	0.88[ASN][1000 genomes]
rs4873119	0.88[ASN][1000 genomes]
rs4873120	0.86[CHB][hapmap]
rs4873123	0.86[CHB][hapmap]
rs4873376	0.81[ASN][1000 genomes]
rs4873379	0.83[ASN][1000 genomes]
rs4873382	0.98[ASN][1000 genomes]
rs4873383	1.00[ASN][1000 genomes]
rs4873388	1.00[ASN][1000 genomes]
rs4873391	1.00[ASN][1000 genomes]
rs4873392	0.88[ASN][1000 genomes]
rs55636909	0.98[ASN][1000 genomes]
rs55879210	0.88[ASN][1000 genomes]
rs55920504	0.95[EUR][1000 genomes]
rs56076516	0.81[EUR][1000 genomes]
rs56659775	1.00[ASN][1000 genomes]
rs57165932	0.81[EUR][1000 genomes]
rs57462717	1.00[ASN][1000 genomes]
rs57585353	0.96[EUR][1000 genomes]
rs58597929	0.95[EUR][1000 genomes]
rs58764084	1.00[ASN][1000 genomes]
rs59379959	1.00[ASN][1000 genomes]
rs59405147	0.95[EUR][1000 genomes]
rs59848488	1.00[ASN][1000 genomes]
rs60061614	0.96[EUR][1000 genomes]
rs60213702	1.00[ASN][1000 genomes]
rs60631955	1.00[ASN][1000 genomes]
rs61662535	1.00[ASN][1000 genomes]
rs6472721	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6472722	0.81[CEU][hapmap]
rs6988440	0.85[ASN][1000 genomes]
rs6994224	1.00[ASN][1000 genomes]
rs7004973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7008449	0.84[ASN][1000 genomes]
rs7008924	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7013903	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72636691	0.81[EUR][1000 genomes]
rs72636696	0.81[EUR][1000 genomes]
rs72636698	0.81[EUR][1000 genomes]
rs72636701	0.81[EUR][1000 genomes]
rs72636702	0.81[EUR][1000 genomes]
rs72638307	0.96[EUR][1000 genomes]
rs72638311	0.96[EUR][1000 genomes]
rs72638312	0.96[EUR][1000 genomes]
rs72638332	0.96[EUR][1000 genomes]
rs72638338	0.95[EUR][1000 genomes]
rs73582706	1.00[ASN][1000 genomes]
rs73582713	1.00[ASN][1000 genomes]
rs73582718	0.98[ASN][1000 genomes]
rs73582724	1.00[ASN][1000 genomes]
rs73582755	1.00[ASN][1000 genomes]
rs73582756	1.00[ASN][1000 genomes]
rs73676017	0.94[ASN][1000 genomes]
rs73676077	0.84[ASN][1000 genomes]
rs7388392	0.97[ASN][1000 genomes]
rs7463456	0.81[ASN][1000 genomes]
rs7825552	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7826013	0.97[ASN][1000 genomes]
rs7828311	1.00[ASN][1000 genomes]
rs7828900	0.84[CHB][hapmap]
rs7831807	0.81[ASN][1000 genomes]
rs9298228	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9298229	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964011	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs967109	0.83[EUR][1000 genomes]
rs967110	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs967116	0.81[CEU][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs971926	0.85[MEX][hapmap]
rs974740	0.88[ASN][1000 genomes]
rs974742	0.88[ASN][1000 genomes]
rs986450	0.81[EUR][1000 genomes]
rs9886451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353749	chr8:50530807-51139242	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1552372	SNTG1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50772800-50775600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:50773000-50773400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
3	chr8:50773000-50774600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr8:50773200-50774400	Enhancers	Brain Germinal Matrix	brain

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