Variant report

Variant	rs1506457
Chromosome Location	chr1:71880016-71880017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1033268	0.86[ASN][1000 genomes]
rs10889916	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs10889918	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1105985	0.85[CHB][hapmap]
rs1112456	0.85[CHB][hapmap]
rs11209780	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs11209782	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1155175	0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs12123319	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12125823	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12135145	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1517760	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2056206	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2421926	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs357245	0.85[CHB][hapmap]
rs4649938	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6424429	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6668512	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs6703162	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs72674979	0.85[ASN][1000 genomes]
rs7516999	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7552024	0.86[ASN][1000 genomes]
rs908686	0.85[ASN][1000 genomes]
rs977145	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs9787180	0.86[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949599	chr1:71655652-72327802	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1005726	chr1:71701840-71953242	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1848377	chr1:71718838-71964514	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv531880	chr1:71724941-71964501	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv830159	chr1:71772308-71909860	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv916508	chr1:71777392-72046388	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv546474	chr1:71793221-72040354	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv461862	chr1:71849037-71937694	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv461873	chr1:71849037-71937694	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv546475	chr1:71849037-71937694	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv830170	chr1:71856447-72008758	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1506457	CTH	cis	cerebellum	SCAN
rs1506457	SRSF11	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71877800-71880800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:71878800-71880800	Enhancers	Fetal Lung	lung
3	chr1:71879000-71880600	Enhancers	Adipose Nuclei	Adipose
4	chr1:71879400-71880600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:71879600-71880400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr1:71879800-71880200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:71879800-71880400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:71879800-71880400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:71879800-71880400	Enhancers	NHDF-Ad	bronchial
10	chr1:71879800-71880600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:71879800-71880600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:71879800-71880800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr1:71879800-71880800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:71880000-71880600	Enhancers	Brain Germinal Matrix	brain

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