Variant report

Variant	rs2693540
Chromosome Location	chr3:158001555-158001556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 161 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs10470472	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10936131	0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs10936132	0.81[ASN][1000 genomes]
rs1095636	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11712563	0.88[ASN][1000 genomes]
rs11715599	0.85[ASN][1000 genomes]
rs11717618	0.84[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11717923	0.81[ASN][1000 genomes]
rs11719153	0.90[ASN][1000 genomes]
rs1193511	0.96[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1193513	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1193536	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1204957	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204960	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12053861	0.84[ASN][1000 genomes]
rs12485440	0.96[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs12486461	0.87[EUR][1000 genomes]
rs12634807	0.84[ASN][1000 genomes]
rs12634832	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12636733	0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs12639261	0.84[ASN][1000 genomes]
rs12639310	0.84[ASN][1000 genomes]
rs12696067	0.96[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs13059066	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13061378	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs13086348	0.80[CEU][hapmap]
rs1581408	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1608100	0.96[CEU][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1608101	0.86[EUR][1000 genomes]
rs1609525	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1609526	0.85[EUR][1000 genomes]
rs1610266	0.91[EUR][1000 genomes]
rs1610267	0.91[EUR][1000 genomes]
rs1610268	0.91[EUR][1000 genomes]
rs1724666	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1724679	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1729998	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1730008	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1730029	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1730032	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1730039	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1730041	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1730044	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1730099	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17683939	0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs1851062	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.99[ASN][1000 genomes]
rs1915935	0.96[CEU][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1918000	0.90[ASN][1000 genomes]
rs2139696	0.96[ASN][1000 genomes]
rs2682402	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682407	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2693546	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34434866	0.84[ASN][1000 genomes]
rs4261830	0.87[EUR][1000 genomes]
rs4317053	0.86[EUR][1000 genomes]
rs4346508	0.96[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4414801	0.87[EUR][1000 genomes]
rs4431056	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4602343	0.87[EUR][1000 genomes]
rs4622858	0.87[EUR][1000 genomes]
rs4642075	0.87[EUR][1000 genomes]
rs4680411	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4680412	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4680421	0.84[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4680425	0.82[ASN][1000 genomes]
rs4680428	0.81[ASN][1000 genomes]
rs58195752	0.81[ASN][1000 genomes]
rs58925169	0.84[ASN][1000 genomes]
rs60962704	0.89[ASN][1000 genomes]
rs6441174	0.87[EUR][1000 genomes]
rs6762706	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6768496	0.80[CEU][hapmap]
rs6770442	0.82[EUR][1000 genomes]
rs6772246	0.81[ASN][1000 genomes]
rs6773505	0.86[EUR][1000 genomes]
rs6784968	0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs6789448	0.87[EUR][1000 genomes]
rs6790608	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6794461	0.86[EUR][1000 genomes]
rs6797626	0.86[EUR][1000 genomes]
rs6800853	0.84[ASN][1000 genomes]
rs6803532	0.87[EUR][1000 genomes]
rs6803630	0.96[CEU][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6807468	0.85[ASN][1000 genomes]
rs696715	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698975	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698976	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698977	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698979	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698981	0.95[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698982	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698983	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698984	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698985	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698991	0.81[YRI][hapmap]
rs698992	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs699918	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs699923	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs699925	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs699926	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73164102	0.87[ASN][1000 genomes]
rs73166358	0.99[ASN][1000 genomes]
rs73168723	0.88[ASN][1000 genomes]
rs73168799	0.86[ASN][1000 genomes]
rs73170303	0.86[ASN][1000 genomes]
rs73170306	0.86[ASN][1000 genomes]
rs73170310	0.81[ASN][1000 genomes]
rs73170326	0.81[ASN][1000 genomes]
rs73170337	0.84[ASN][1000 genomes]
rs73170339	0.84[ASN][1000 genomes]
rs73170346	0.84[ASN][1000 genomes]
rs73170364	0.84[ASN][1000 genomes]
rs7614572	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7618071	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7622971	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7623107	0.80[CEU][hapmap]
rs7624303	0.93[CHD][hapmap]
rs7630176	0.96[CEU][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7645475	0.83[CEU][hapmap]
rs7647342	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7653039	0.83[EUR][1000 genomes]
rs827104	0.96[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs827130	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs827139	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827141	0.96[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs827142	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs827145	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs827146	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs827147	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs827149	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs827153	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs827155	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs827157	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs827160	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs827162	0.93[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs827168	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs827170	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs827173	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs827174	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs827801	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs827805	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs844141	0.84[EUR][1000 genomes]
rs860422	0.86[EUR][1000 genomes]
rs862352	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs864331	0.92[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs864876	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs866657	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9290020	0.85[EUR][1000 genomes]
rs9290021	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9814942	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9820954	0.87[EUR][1000 genomes]
rs9848433	0.85[EUR][1000 genomes]
rs9870745	0.84[EUR][1000 genomes]
rs9871021	0.80[EUR][1000 genomes]
rs9881063	0.96[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2693540	SLC33A1	cis	cerebellum	SCAN
rs2693540	RP11-538P18.2	cis	lung	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157986200-158006600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:157986400-158040000	Weak transcription	Primary B cells from cord blood	blood
3	chr3:157988200-158009600	Weak transcription	Pancreas	Pancrea
4	chr3:157988400-158001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:157993400-158054600	Weak transcription	Primary T cells from cord blood	blood
6	chr3:157993800-158040600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:157996400-158001600	Weak transcription	K562	blood
8	chr3:157998000-158023400	Weak transcription	Primary monocytes fromperipheralblood	blood

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