Variant report

Variant	rs59990581
Chromosome Location	chr1:223881577-223881578
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	chr1:223877078..223879115-chr1:223880741..223883730,2	K562	blood:
2	chr1:223575927..223578563-chr1:223880828..223883618,2	K562	blood:

Variant related genes	Relation type
ENSG00000212398	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10799550	0.88[EUR][1000 genomes]
rs12567519	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568612	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17556570	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1936525	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41307690	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4511081	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653522	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61822582	0.85[EUR][1000 genomes]
rs61822583	0.86[EUR][1000 genomes]
rs61822586	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61822630	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61822631	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61822632	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61822633	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61822634	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61822635	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61822636	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823962	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823965	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61823967	0.80[EUR][1000 genomes]
rs61823968	0.80[EUR][1000 genomes]
rs6656416	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6690568	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6702314	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6702430	0.90[EUR][1000 genomes]
rs7551783	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59990581	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223876400-223885600	Weak transcription	A549	lung
2	chr1:223878800-223884000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:223881400-223881800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:223881400-223884200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links