Variant report

Variant	rs281959
Chromosome Location	chr1:91742055-91742056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10493845	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs10801850	0.89[AMR][1000 genomes]
rs10801851	0.85[YRI][hapmap]
rs10801862	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs10923010	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs1158436	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12562636	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12564233	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs12568483	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1307751	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1583817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1583818	0.93[ASW][hapmap];0.83[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1595868	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131417	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs1822056	0.85[YRI][hapmap]
rs192519	0.89[CHD][hapmap];0.92[JPT][hapmap]
rs2033915	0.86[AMR][1000 genomes]
rs281935	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs281956	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs281966	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs281968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs281979	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs281990	0.89[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs281992	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs281996	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs281997	0.92[JPT][hapmap]
rs281998	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4658220	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4658221	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4658222	1.00[JPT][hapmap]
rs582737	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59973709	0.91[ASN][1000 genomes]
rs628897	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs661989	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67274437	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs678752	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs681589	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs683765	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs694581	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72726276	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7417055	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs876761	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9324372	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs9660037	0.89[ASN][1000 genomes]
rs9662393	0.89[ASN][1000 genomes]
rs9724763	0.87[ASN][1000 genomes]
rs988203	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[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	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv1800676	chr1:91722083-91854389	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv1796351	chr1:91722083-91872374	Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs281959	SNORD21	cis	cerebellum	SCAN
rs281959	CCDC18	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91717000-91743000	Weak transcription	Fetal Lung	lung
2	chr1:91719600-91748400	Weak transcription	Ovary	ovary
3	chr1:91719800-91748000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:91732400-91744200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:91738200-91748400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:91739800-91743400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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