Variant report

Variant	rs4019558
Chromosome Location	chr2:179270883-179270884
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179269194..179271772-chr2:179274034..179275592,2	K562	blood:
2	chr2:179269516..179271949-chr2:179276135..179277848,2	K562	blood:
3	chr2:179270312..179272501-chr2:179279008..179282360,3	K562	blood:
4	chr2:179270737..179273454-chr2:179278076..179279839,2	MCF-7	breast:
5	chr2:179267808..179270884-chr2:179270980..179273885,4	K562	blood:
6	chr2:179267516..179271156-chr2:179271366..179274621,4	K562	blood:

Variant related genes	Relation type
ENSG00000223960	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10173183	0.88[EUR][1000 genomes]
rs1017397	0.83[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10201175	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10204497	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688081	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1560870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276617	0.87[EUR][1000 genomes]
rs2366601	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4404314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6757186	0.90[EUR][1000 genomes]
rs723841	0.87[EUR][1000 genomes]
rs728005	0.93[GIH][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7589565	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7605289	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8179648	0.91[YRI][hapmap]
rs890579	0.80[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs919177	0.90[EUR][1000 genomes]
rs9288019	0.91[TSI][hapmap]
rs9967820	0.91[YRI][hapmap]
rs9973732	0.87[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4019558	CIR1	cis	cerebellum	SCAN
rs4019558	ATP5G3	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179268400-179271000	Enhancers	HSMMtube	muscle
2	chr2:179269200-179271800	Weak transcription	NHLF	lung
3	chr2:179269400-179271800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:179269400-179271800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:179269400-179277600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:179269600-179271000	Enhancers	GM12878-XiMat	blood
7	chr2:179269600-179271800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:179269600-179271800	Weak transcription	NHDF-Ad	bronchial
9	chr2:179270000-179271800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:179270000-179277800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:179270000-179277800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:179270600-179271000	Enhancers	K562	blood
13	chr2:179270600-179277800	Weak transcription	HSMM	muscle

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