Variant report

Variant	rs2792664
Chromosome Location	chr1:76459445-76459446
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10732724	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10873804	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs10873863	0.84[CEU][hapmap]
rs11161887	0.81[JPT][hapmap]
rs11162053	0.90[ASN][1000 genomes]
rs11162066	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs1146648	0.81[CHD][hapmap]
rs12024645	0.83[CHD][hapmap]
rs12044211	0.82[CHB][hapmap]
rs12064158	0.90[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs12076093	0.81[CHD][hapmap]
rs12095069	0.90[ASN][1000 genomes]
rs12402347	0.87[ASN][1000 genomes]
rs12405994	0.87[ASN][1000 genomes]
rs12407107	0.83[CHD][hapmap]
rs12408897	0.87[ASN][1000 genomes]
rs12409592	0.82[CHD][hapmap]
rs12410373	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs12410724	0.90[ASN][1000 genomes]
rs1251272	0.81[CHD][hapmap]
rs1251531	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251539	0.90[ASN][1000 genomes]
rs1251550	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251556	0.90[ASN][1000 genomes]
rs1251560	0.91[ASN][1000 genomes]
rs1251579	0.82[ASN][1000 genomes]
rs1251580	0.82[ASN][1000 genomes]
rs1251581	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251587	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251588	0.82[ASN][1000 genomes]
rs1251591	0.81[ASN][1000 genomes]
rs1251594	0.81[ASN][1000 genomes]
rs12567390	0.85[CHB][hapmap]
rs12732495	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1340684	0.89[ASN][1000 genomes]
rs1361487	0.85[ASN][1000 genomes]
rs1417402	0.87[ASN][1000 genomes]
rs1438175	0.90[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs1438176	0.90[ASN][1000 genomes]
rs1498313	0.85[CEU][hapmap];0.97[CHD][hapmap]
rs1658737	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1658739	0.92[CEU][hapmap]
rs1689271	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap]
rs17097681	0.80[JPT][hapmap]
rs17097695	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs17097821	0.90[ASN][1000 genomes]
rs17097836	0.90[ASN][1000 genomes]
rs17097837	0.90[ASN][1000 genomes]
rs17097841	0.90[ASN][1000 genomes]
rs17097863	0.90[ASN][1000 genomes]
rs17097864	0.90[ASN][1000 genomes]
rs17097867	0.89[ASN][1000 genomes]
rs17649675	0.82[CHB][hapmap]
rs1770876	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770880	0.84[AFR][1000 genomes]
rs1796799	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796812	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.81[ASN][1000 genomes]
rs1890967	0.90[ASN][1000 genomes]
rs1938321	0.86[ASN][1000 genomes]
rs1938322	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938323	0.90[ASN][1000 genomes]
rs2047435	0.81[CHD][hapmap]
rs2066213	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2307077	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap]
rs34574524	0.90[ASN][1000 genomes]
rs35290302	0.83[CHD][hapmap]
rs3737574	0.83[CHD][hapmap]
rs3795251	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs3920847	0.87[ASN][1000 genomes]
rs4949619	0.90[ASN][1000 genomes]
rs4949685	0.90[ASN][1000 genomes]
rs5745429	0.80[CHD][hapmap]
rs5745451	0.81[JPT][hapmap]
rs5745523	0.80[JPT][hapmap]
rs5745542	0.80[JPT][hapmap]
rs5745546	0.81[JPT][hapmap]
rs7418941	0.87[ASN][1000 genomes]
rs7524665	0.81[ASN][1000 genomes]
rs7545057	0.82[CHB][hapmap]
rs931506	0.84[CHB][hapmap];0.85[JPT][hapmap]

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	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2792664	SNORD45B	cis	cerebellum	SCAN
rs2792664	ACADM	cis	parietal	SCAN
rs2792664	MSH4	cis	parietal	SCAN
rs2792664	SNORD45B	cis	parietal	SCAN
rs2792664	MSH4	cis	Artery Tibial	GTEx
rs2792664	ACADM	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76458200-76466600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:76459200-76461000	Enhancers	Fetal Lung	lung

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