Variant report

Variant	rs11162685
Chromosome Location	chr1:79780054-79780055
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10732727	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10735756	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10735757	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10747361	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10874032	0.84[AMR][1000 genomes]
rs11162675	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11162678	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11162684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162686	0.91[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs11162695	0.81[ASN][1000 genomes]
rs11162696	0.81[ASN][1000 genomes]
rs11162697	0.81[ASN][1000 genomes]
rs12027436	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12127263	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12732505	0.81[ASN][1000 genomes]
rs12734357	0.81[ASN][1000 genomes]
rs12749224	0.81[ASN][1000 genomes]
rs1331707	0.88[AMR][1000 genomes]
rs1331709	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs1331713	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1331714	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1331716	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1331718	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1331723	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1412129	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1412130	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1412131	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1412132	0.89[AMR][1000 genomes]
rs1412133	0.88[AMR][1000 genomes]
rs1412134	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1412135	0.89[AMR][1000 genomes]
rs1412137	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412139	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1888766	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1929622	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2039339	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs228471	0.81[ASN][1000 genomes]
rs228481	0.81[ASN][1000 genomes]
rs228488	0.81[ASN][1000 genomes]
rs2882993	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2989850	0.80[AMR][1000 genomes]
rs3015124	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3015126	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34146004	0.81[ASN][1000 genomes]
rs34510598	0.81[ASN][1000 genomes]
rs35676104	0.81[ASN][1000 genomes]
rs35733452	0.81[ASN][1000 genomes]
rs3915745	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4414002	0.81[ASN][1000 genomes]
rs4630085	0.81[ASN][1000 genomes]
rs4650405	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5012068	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424649	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6661645	0.81[ASN][1000 genomes]
rs7515632	0.84[AMR][1000 genomes]
rs7528017	0.81[AMR][1000 genomes]
rs7542083	0.81[AMR][1000 genomes]
rs7546136	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7546200	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7553187	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv871182	chr1:79614989-79822735	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	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
4	nsv870962	chr1:79755185-79835066	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11162685	SNORD45C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79778000-79781600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:79780000-79781400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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