Variant report

Variant	rs2849977
Chromosome Location	chr21:28406107-28406108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1012766	0.97[ASN][1000 genomes]
rs1041422	0.99[ASN][1000 genomes]
rs11911372	0.99[ASN][1000 genomes]
rs12185828	0.99[ASN][1000 genomes]
rs12626439	0.91[ASN][1000 genomes]
rs13046394	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1497276	0.91[ASN][1000 genomes]
rs1603557	0.97[ASN][1000 genomes]
rs1603558	0.95[ASN][1000 genomes]
rs1812603	0.97[ASN][1000 genomes]
rs1812604	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs189204	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2187293	0.85[ASN][1000 genomes]
rs2212816	0.85[ASN][1000 genomes]
rs2212818	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs233579	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233580	0.93[ASN][1000 genomes]
rs233583	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233584	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233586	0.85[ASN][1000 genomes]
rs233590	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs233593	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs233595	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs233606	0.90[ASN][1000 genomes]
rs233610	0.85[ASN][1000 genomes]
rs233614	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs233615	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs233616	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233621	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233622	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2830639	0.96[ASN][1000 genomes]
rs2830641	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2830642	0.97[ASN][1000 genomes]
rs2830643	0.97[ASN][1000 genomes]
rs2830644	0.97[ASN][1000 genomes]
rs2830645	0.99[ASN][1000 genomes]
rs2830649	0.91[ASN][1000 genomes]
rs2830650	0.93[ASN][1000 genomes]
rs2830651	0.93[ASN][1000 genomes]
rs2830655	0.85[ASN][1000 genomes]
rs2830659	0.82[ASN][1000 genomes]
rs2849665	0.94[ASN][1000 genomes]
rs371445	0.83[ASN][1000 genomes]
rs374915	0.93[ASN][1000 genomes]
rs381814	0.87[ASN][1000 genomes]
rs406835	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4143412	0.96[ASN][1000 genomes]
rs417783	0.82[ASN][1000 genomes]
rs420911	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs429133	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs432557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs437747	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs449156	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs452337	0.87[ASN][1000 genomes]
rs479335	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544362	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs563108	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs566699	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs575467	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs577332	0.94[ASN][1000 genomes]
rs578835	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs580945	0.83[ASN][1000 genomes]
rs6516750	0.97[ASN][1000 genomes]
rs653105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs656754	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs658034	0.83[ASN][1000 genomes]
rs667362	0.93[ASN][1000 genomes]
rs667756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs678227	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs680466	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7275831	0.82[ASN][1000 genomes]
rs7278373	0.85[ASN][1000 genomes]
rs7278482	0.83[ASN][1000 genomes]
rs7278648	0.85[ASN][1000 genomes]
rs7279417	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7282307	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7283451	0.86[ASN][1000 genomes]
rs8126694	0.99[ASN][1000 genomes]
rs8134115	1.00[ASN][1000 genomes]
rs8134126	1.00[ASN][1000 genomes]
rs9305296	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9976168	0.97[ASN][1000 genomes]
rs9979645	0.97[ASN][1000 genomes]
rs9980759	0.83[ASN][1000 genomes]
rs9984610	0.97[ASN][1000 genomes]
rs9984674	0.97[ASN][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	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2758532	chr21:28380230-28540443	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	esv2758817	chr21:28380230-28540443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	nsv1066134	chr21:28382038-28406482	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
5	nsv1055852	chr21:28382038-28407515	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
6	nsv587341	chr21:28391743-28419053	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2849977	ADAMTS5	cis	cerebellum	SCAN
rs2849977	APP	cis	parietal	SCAN
rs2849977	MRPL39	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28351800-28416600	Weak transcription	Ovary	ovary
2	chr21:28399200-28408200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr21:28406000-28406200	Enhancers	Fetal Brain Female	brain

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