Variant report

Variant	rs2408554
Chromosome Location	chr13:52683263-52683264
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52682568..52684344-chr13:52687301..52689762,2	K562	blood:

Extended variants
information (count: 129 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1004576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1055062	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1060631	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1134727	0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11620583	0.87[CHB][hapmap]
rs12146904	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.99[ASN][1000 genomes]
rs12431310	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12560598	0.90[ASN][1000 genomes]
rs1571189	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1801243	0.91[CHB][hapmap]
rs1886538	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs1886539	0.97[ASN][1000 genomes]
rs1886542	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1886543	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1886544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1886545	0.92[ASN][1000 genomes]
rs1886546	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1886547	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1924611	0.86[CHB][hapmap]
rs2004866	0.91[CHB][hapmap]
rs2005182	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2147363	0.83[CEU][hapmap]
rs2181891	0.91[CHB][hapmap]
rs2274202	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2277448	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296347	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2296348	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2296349	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408544	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408546	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2408547	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408548	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408550	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408551	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408552	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2408609	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408611	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2897964	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2897965	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2897977	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs3368	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs3742289	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3742291	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3783240	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs3783242	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3818422	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3825528	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs4261421	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4264295	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4297592	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs4497567	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs4941727	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4943060	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61958804	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61958805	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6561656	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6561658	0.86[CHB][hapmap]
rs6650384	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6650385	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66849828	0.94[ASN][1000 genomes]
rs7318287	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7319784	0.88[ASN][1000 genomes]
rs7320252	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7320429	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs732071	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs7320831	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7321120	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[ASN][1000 genomes]
rs7321310	0.88[ASN][1000 genomes]
rs7321435	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs7321775	0.80[ASN][1000 genomes]
rs7324458	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7327634	0.91[CHB][hapmap]
rs7332356	0.91[ASN][1000 genomes]
rs7338131	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs747781	0.91[CHB][hapmap]
rs755363	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7981904	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7991237	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7995946	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7998770	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316563	0.87[CHB][hapmap]
rs9526819	0.87[CHB][hapmap]
rs9526823	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526825	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526826	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526834	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526835	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526836	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526837	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9526841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9526842	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9526843	0.97[ASN][1000 genomes]
rs9535812	0.91[CHB][hapmap]
rs9535822	0.86[CHB][hapmap]
rs9535825	0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap]
rs9535826	0.87[CHB][hapmap]
rs9535832	0.91[CHB][hapmap]
rs9535836	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9535845	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535851	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9535853	0.91[ASN][1000 genomes]
rs9535856	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9535858	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9535861	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535862	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9535866	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9535867	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535871	0.94[ASN][1000 genomes]
rs9535873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535878	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9535879	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9535880	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9535882	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9535883	0.90[ASN][1000 genomes]
rs9535885	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs9535887	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9535888	0.85[ASN][1000 genomes]
rs9535889	0.91[ASN][1000 genomes]
rs9563089	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9568682	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs9568684	0.86[CEU][hapmap];0.88[JPT][hapmap]
rs9568692	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568713	0.91[CHB][hapmap];0.81[JPT][hapmap]

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	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2408554	NEK5	cis	cerebellum	SCAN
rs2408554	CKAP2	cis	parietal	SCAN
rs2408554	NCRNA00282	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52682200-52684600	Enhancers	Fetal Intestine Large	intestine
2	chr13:52682800-52684000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:52683000-52683600	Enhancers	Fetal Intestine Small	intestine

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