Variant report

Variant	rs2157057
Chromosome Location	chr3:46366269-46366270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10865940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11711054	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923720	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13081845	0.85[EUR][1000 genomes]
rs13084656	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs13096142	0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs1388604	0.90[JPT][hapmap]
rs1799865	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2097282	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2097284	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2157058	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2157059	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187669	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2187670	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2213291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213292	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3092962	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs3092963	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3138042	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34148191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34193387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34505903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34997146	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35053103	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35465430	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35510257	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35675823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35971655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36030342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36048784	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3762823	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs3918358	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4134396	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683198	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683211	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4683215	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4683218	0.82[ASN][1000 genomes]
rs62244813	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62244827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62244828	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62244840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62244848	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441950	0.90[JPT][hapmap]
rs6441953	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441958	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6441959	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6441960	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6441961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441963	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6441964	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441971	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs6441972	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6767895	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775208	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783993	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6785878	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6785981	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6788723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6794300	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6802288	0.83[EUR][1000 genomes]
rs71615444	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7371987	0.90[JPT][hapmap];0.81[MEX][hapmap]
rs7372094	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7374654	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7374671	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7432080	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs743660	0.81[MEX][hapmap]
rs7612940	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7626249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762789	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7634816	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7635588	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs963045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813756	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9842716	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs9852052	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9853223	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs9856098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9875668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	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
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2157057	SLC25A20	cis	cerebellum	SCAN
rs2157057	KLHL18	cis	parietal	SCAN
rs2157057	TRAIP	cis	cerebellum	SCAN
rs2157057	ABHD5	cis	parietal	SCAN
rs2157057	CCR5	trans	multi-tissue	Pritchard
rs2157057	DALRD3	cis	cerebellum	SCAN
rs2157057	RBM5	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46350800-46367600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:46364400-46366800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:46364400-46367000	ZNF genes & repeats	GM12878-XiMat	blood
4	chr3:46365000-46366400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr3:46365600-46367600	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr3:46366200-46366800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:46366200-46368200	Enhancers	Dnd41	blood

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