Variant report

Variant	rs2424555
Chromosome Location	chr20:23417705-23417706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr20:23417499-23417723	GM12878	blood:	n/a	chr20:23417540-23417553 chr20:23417542-23417553
2	ELF1	chr20:23417325-23417709	K562	blood:	n/a	chr20:23417476-23417489 chr20:23417540-23417553 chr20:23417542-23417553

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23336129..23338538-chr20:23416708..23418719,2	K562	blood:
2	chr20:23342185..23344395-chr20:23415797..23420151,3	K562	blood:

Variant related genes	Relation type
CSTL1	TF binding region
ENSG00000125812	Chromatin interaction
ENSG00000232645	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1016628	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12349	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1419007	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2024746	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2180139	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236023	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2243448	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2253834	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2281431	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2295239	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2424527	0.91[EUR][1000 genomes]
rs2424542	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2424559	0.82[EUR][1000 genomes]
rs3746736	0.82[EUR][1000 genomes]
rs4142246	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815198	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6048750	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6048760	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6048779	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6048781	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048784	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6076055	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6083114	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6083127	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6137933	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs761723	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs999068	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[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	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv912818	chr20:23406519-23567838	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv912819	chr20:23406519-23569400	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv912820	chr20:23406519-23578148	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1065390	chr20:23412890-23569238	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1065719	chr20:23415029-23565333	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv544214	chr20:23415029-23565333	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2424555	NAPB	cis	Skin Sun Exposed Lower leg	GTEx
rs2424555	NAPB	cis	Artery Tibial	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23415800-23417800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr20:23415800-23417800	Enhancers	Fetal Muscle Trunk	muscle
3	chr20:23416400-23417800	Enhancers	Fetal Intestine Small	intestine
4	chr20:23416400-23417800	Enhancers	Stomach Mucosa	stomach
5	chr20:23416600-23417800	Enhancers	Right Atrium	heart
6	chr20:23416800-23417800	Enhancers	Fetal Intestine Large	intestine
7	chr20:23416800-23417800	Enhancers	Ovary	ovary
8	chr20:23417000-23422800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr20:23417200-23417800	Enhancers	Brain Cingulate Gyrus	brain
10	chr20:23417200-23434800	Weak transcription	Gastric	stomach
11	chr20:23417400-23417800	Enhancers	Liver	Liver
12	chr20:23417400-23417800	Enhancers	Brain Substantia Nigra	brain
13	chr20:23417600-23417800	Enhancers	Brain Hippocampus Middle	brain
14	chr20:23417600-23417800	Flanking Active TSS	K562	blood
15	chr20:23417600-23418200	Enhancers	HepG2	liver
16	chr20:23417600-23422400	Weak transcription	Brain Anterior Caudate	brain

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