Variant report

Variant	rs2424476
Chromosome Location	chr20:22767280-22767281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:22766590..22768153-chr20:22786046..22787967,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1761	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2092660	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2143902	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2179856	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2179859	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404493	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424461	0.93[EUR][1000 genomes]
rs2424464	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2424465	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2424466	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2424468	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2424469	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2424470	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2424473	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2424475	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331580	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4516506	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4815144	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6075947	0.95[EUR][1000 genomes]
rs6075948	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6082814	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6113803	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6113810	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv544213	chr20:22722740-22791150	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv528221	chr20:22732749-22767280	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv912816	chr20:22757960-23062927	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv520547	chr20:22767280-22771404	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2424476	GINS1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22758000-22772000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:22761000-22768800	Weak transcription	Aorta	Aorta
3	chr20:22764800-22770200	Weak transcription	Right Atrium	heart
4	chr20:22767200-22767400	Enhancers	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links