Variant report

Variant	rs10045601
Chromosome Location	chr5:119907360-119907361
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1037572	0.93[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1039546	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519637	0.93[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs11241548	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11241549	1.00[CEU][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1157177	0.93[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.87[EUR][1000 genomes]
rs1157178	0.93[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs13165484	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs13170550	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13171101	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1454981	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1524576	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2124162	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs2168215	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs300966	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4895262	0.93[CEU][hapmap];0.91[GIH][hapmap];0.86[EUR][1000 genomes]
rs6862351	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7706727	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs874946	0.93[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830463	chr5:119806643-119968825	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv462427	chr5:119838923-119928674	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599601	chr5:119838923-119928674	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1031453	chr5:119843593-120393038	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv948613	chr5:119861955-119999008	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv599602	chr5:119866504-120023393	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv949499	chr5:119869763-119999008	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv882787	chr5:119874306-119925692	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10045601	SNX2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119894600-119908200	Weak transcription	Fetal Lung	lung
2	chr5:119904800-119913200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:119904800-119931200	Weak transcription	Osteobl	bone
4	chr5:119905000-119925800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:119905200-119907600	Weak transcription	HSMM	muscle
6	chr5:119905200-119908400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:119905400-119907400	Weak transcription	NHDF-Ad	bronchial
8	chr5:119905400-119907800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:119905600-119934600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:119907200-119908000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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