Variant report

Variant	rs12560598
Chromosome Location	chr13:52619717-52619718
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	chr13:52605847..52608629-chr13:52617220..52620408,3	K562	blood:
2	chr13:52618736..52621348-chr13:52625262..52627911,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1004576	0.90[ASN][1000 genomes]
rs1055062	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1060631	0.90[ASN][1000 genomes]
rs1134727	0.89[ASN][1000 genomes]
rs12146904	0.90[ASN][1000 genomes]
rs12431310	0.90[ASN][1000 genomes]
rs1571189	0.83[ASN][1000 genomes]
rs1886539	0.88[ASN][1000 genomes]
rs1886543	0.90[ASN][1000 genomes]
rs1886544	0.90[ASN][1000 genomes]
rs1886545	0.90[ASN][1000 genomes]
rs1886546	0.90[ASN][1000 genomes]
rs2005182	0.91[ASN][1000 genomes]
rs2277448	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2296347	0.88[ASN][1000 genomes]
rs2408546	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2408547	0.94[ASN][1000 genomes]
rs2408548	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2408552	0.88[ASN][1000 genomes]
rs2408554	0.90[ASN][1000 genomes]
rs2897964	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2897965	0.86[ASN][1000 genomes]
rs3742289	0.90[ASN][1000 genomes]
rs3742291	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3783242	0.89[ASN][1000 genomes]
rs3818422	0.89[ASN][1000 genomes]
rs4261421	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4264295	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4941727	0.84[ASN][1000 genomes]
rs4943060	0.86[ASN][1000 genomes]
rs61958804	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs61958805	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6561656	0.87[ASN][1000 genomes]
rs6650384	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6650385	0.94[ASN][1000 genomes]
rs66849828	0.84[ASN][1000 genomes]
rs7318287	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7319784	0.87[ASN][1000 genomes]
rs7320252	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7320429	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs732071	0.80[AMR][1000 genomes]
rs7320831	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7321120	0.87[ASN][1000 genomes]
rs7321310	0.87[ASN][1000 genomes]
rs7324458	0.90[ASN][1000 genomes]
rs7332356	0.90[ASN][1000 genomes]
rs7338131	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7998770	0.90[ASN][1000 genomes]
rs9526823	0.90[ASN][1000 genomes]
rs9526825	0.91[ASN][1000 genomes]
rs9526826	0.94[ASN][1000 genomes]
rs9526834	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526835	0.86[ASN][1000 genomes]
rs9526836	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526841	0.88[ASN][1000 genomes]
rs9526843	0.88[ASN][1000 genomes]
rs9535845	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9535853	0.90[ASN][1000 genomes]
rs9535861	0.81[ASN][1000 genomes]
rs9535867	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535871	0.85[ASN][1000 genomes]
rs9535873	0.90[ASN][1000 genomes]
rs9535883	0.83[ASN][1000 genomes]
rs9535889	0.83[ASN][1000 genomes]
rs9568692	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12560598	NEK3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52600400-52627600	Weak transcription	HSMMtube	muscle
2	chr13:52610400-52620800	Weak transcription	Left Ventricle	heart
3	chr13:52618200-52619800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links