Variant report

Variant	rs3000178
Chromosome Location	chr1:79877035-79877036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11162686	0.87[CHB][hapmap];0.85[CHD][hapmap]
rs11162695	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11162696	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11162697	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11578751	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11588913	0.80[ASN][1000 genomes]
rs11591000	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12724768	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12726250	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12727530	0.80[ASN][1000 genomes]
rs12732505	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12734357	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12739748	0.81[EUR][1000 genomes]
rs12739762	0.83[EUR][1000 genomes]
rs12745266	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12749113	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12749224	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12754109	0.88[ASN][1000 genomes]
rs12760991	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1331709	0.93[CHB][hapmap];0.85[CHD][hapmap]
rs1353290	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1389942	0.81[CEU][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs1389946	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1494843	0.83[ASN][1000 genomes]
rs1494852	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1494856	0.80[ASN][1000 genomes]
rs1494865	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17417360	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17418410	0.85[ASN][1000 genomes]
rs17418579	0.80[ASN][1000 genomes]
rs17451181	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17451905	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2029788	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2101800	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2132055	0.85[ASN][1000 genomes]
rs2132057	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2860503	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2934867	0.83[ASN][1000 genomes]
rs2934873	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2934878	0.85[EUR][1000 genomes]
rs3000098	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3000110	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3000133	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3000155	0.82[EUR][1000 genomes]
rs3000174	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3000175	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3000176	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3000177	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3000179	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3015006	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3015008	0.85[EUR][1000 genomes]
rs3015013	0.81[EUR][1000 genomes]
rs3015025	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3015098	0.90[AMR][1000 genomes]
rs3015107	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3015108	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015120	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33944981	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34146004	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34322872	0.83[ASN][1000 genomes]
rs34510598	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34554398	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35352017	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35490451	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35676104	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35706038	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35707904	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35733452	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35963120	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36033983	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4414002	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4506421	0.92[CHB][hapmap]
rs4604653	0.85[ASN][1000 genomes]
rs4630085	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58635031	0.83[ASN][1000 genomes]
rs61031256	0.83[ASN][1000 genomes]
rs61767574	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66530141	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6661645	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6692670	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6699018	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7516261	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7527570	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7536196	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7536365	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555044	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870657	chr1:79701220-79890774	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830337	chr1:79791879-79913241	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv546633	chr1:79794719-79877035	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv871649	chr1:79807447-79924175	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1004014	chr1:79811049-80042309	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv462161	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv462173	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv470721	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv546635	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3000178	USP33	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79876600-79877200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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