Variant report

Variant	rs4846724
Chromosome Location	chr1:221967817-221967818
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	chr1:221959363..221962341-chr1:221966236..221967931,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10495177	0.90[ASN][1000 genomes]
rs10863658	0.95[ASN][1000 genomes]
rs11588738	0.92[ASN][1000 genomes]
rs12029988	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs12040332	0.93[ASN][1000 genomes]
rs12565255	0.92[ASN][1000 genomes]
rs12568507	0.93[ASN][1000 genomes]
rs12726313	0.83[ASN][1000 genomes]
rs3003886	0.91[ASN][1000 genomes]
rs3010839	0.94[EUR][1000 genomes]
rs3010840	0.94[EUR][1000 genomes]
rs34557512	0.85[ASN][1000 genomes]
rs35907150	0.97[ASN][1000 genomes]
rs3934723	0.90[ASN][1000 genomes]
rs4240927	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4240929	0.95[ASN][1000 genomes]
rs4297303	0.83[ASN][1000 genomes]
rs4846723	0.97[ASN][1000 genomes]
rs4846726	0.96[ASN][1000 genomes]
rs6604671	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7523844	0.82[ASN][1000 genomes]
rs7526577	0.82[ASN][1000 genomes]
rs9441956	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv873201	chr1:221956626-222007535	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv947161	chr1:221967491-221977571	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4846724	C1orf58	cis	cerebellum	SCAN
rs4846724	USH2A	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221960400-221970000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:221964600-221969200	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:221966400-221968200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:221966600-221968200	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr1:221966800-221968200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:221967000-221968600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:221967200-221968000	Enhancers	HMEC	breast
8	chr1:221967200-221968200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr1:221967200-221968400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:221967200-221968600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:221967400-222009800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:221967600-221968400	Enhancers	Primary B cells from cord blood	blood
13	chr1:221967600-221969000	Enhancers	GM12878-XiMat	blood
14	chr1:221967800-221968000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:221967800-221970600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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