Variant report

Variant	rs6441960
Chromosome Location	chr3:46351874-46351875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1034382	0.88[EUR][1000 genomes]
rs10865940	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11130089	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11711054	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13084656	0.85[JPT][hapmap]
rs13096142	0.85[JPT][hapmap]
rs1388604	0.95[JPT][hapmap]
rs1979672	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs2040389	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2040390	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2097283	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2157057	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2157058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2157059	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2187669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2187670	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2213288	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2213291	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2213292	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2373226	0.90[EUR][1000 genomes]
rs3092962	0.95[CEU][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3092964	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34148191	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34193387	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34505903	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34997146	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35053103	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35465430	0.88[AMR][1000 genomes]
rs35510257	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35675823	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35971655	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs36030342	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs36048784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36118141	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3762823	0.95[CEU][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3918359	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3918361	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41276529	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4134396	0.83[ASN][1000 genomes]
rs41418050	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41502550	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4682812	0.81[AMR][1000 genomes]
rs4683194	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683199	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683211	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683215	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683218	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62244813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62244827	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62244840	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62244848	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6441950	0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441958	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441959	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441961	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6441962	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6441963	0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6441964	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6441968	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6441971	0.95[CEU][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs67450950	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6765031	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6767895	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6771900	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6775208	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6783993	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785878	0.81[ASN][1000 genomes]
rs6788723	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6788849	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6794300	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6801761	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6810232	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71327045	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7371987	0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7372094	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7374654	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7374671	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7432080	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs743660	0.95[CEU][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs7612940	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626249	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7634816	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7635588	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs768539	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs963045	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9813756	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9818053	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9839623	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9840204	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9842716	0.85[JPT][hapmap]
rs9852052	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9853223	0.84[JPT][hapmap]
rs9856098	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9875668	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9877860	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6441960	SLC25A20	cis	cerebellum	SCAN
rs6441960	ABHD5	cis	parietal	SCAN
rs6441960	CXCR6	cis	parietal	SCAN
rs6441960	DALRD3	cis	cerebellum	SCAN
rs6441960	SS18L2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46350600-46352400	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr3:46350800-46367600	Enhancers	Primary monocytes fromperipheralblood	blood

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