Variant report

Variant	rs6533438
Chromosome Location	chr4:110538429-110538430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10006897	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10010159	0.82[ASN][1000 genomes]
rs10017027	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1029449	0.82[ASN][1000 genomes]
rs1029450	0.82[ASN][1000 genomes]
rs1029451	0.82[ASN][1000 genomes]
rs11098036	0.80[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11098039	0.81[ASN][1000 genomes]
rs11098040	0.81[ASN][1000 genomes]
rs11937120	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12504784	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs12511995	0.81[ASN][1000 genomes]
rs12646055	0.84[CEU][hapmap];0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs13103167	0.85[CEU][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap]
rs1476545	0.83[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs197203	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs197231	0.81[CEU][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs197235	0.82[ASN][1000 genomes]
rs2079131	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2107051	0.85[CEU][hapmap];0.81[ASN][1000 genomes]
rs3181191	0.88[GIH][hapmap];0.81[TSI][hapmap]
rs34925690	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35838666	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3733611	0.81[CHD][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs3756256	0.82[ASN][1000 genomes]
rs4698744	0.85[CEU][hapmap];0.81[ASN][1000 genomes]
rs4698776	0.85[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap]
rs4698780	0.81[CHD][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs60916792	0.81[ASN][1000 genomes]
rs6533444	0.81[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6533445	0.81[CHD][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs6815377	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6816926	0.82[ASN][1000 genomes]
rs6825095	0.81[ASN][1000 genomes]
rs6831930	0.81[ASN][1000 genomes]
rs6833490	0.82[ASN][1000 genomes]
rs6834701	0.82[ASN][1000 genomes]
rs6849691	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6851190	0.81[ASN][1000 genomes]
rs6851356	0.80[ASN][1000 genomes]
rs6856535	0.82[ASN][1000 genomes]
rs726583	0.82[ASN][1000 genomes]
rs726584	0.82[ASN][1000 genomes]
rs726585	0.81[CHD][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs735642	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs763370	0.85[CEU][hapmap]
rs7676806	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7699736	0.82[ASN][1000 genomes]
rs9990765	0.82[ASN][1000 genomes]
rs9993532	0.82[ASN][1000 genomes]
rs9996648	0.82[ASN][1000 genomes]
rs9996730	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv3419480	chr4:110521397-110549622	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6533438	CASP6	cis	parietal	SCAN
rs6533438	CASP6	cis	cerebellum	SCAN
rs6533438	ANK2	cis	cerebellum	SCAN
rs6533438	LARP7	cis	parietal	SCAN
rs6533438	SGMS2	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110531000-110546000	Weak transcription	Esophagus	oesophagus
2	chr4:110531000-110550600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:110531400-110546000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:110531400-110546000	Weak transcription	Spleen	Spleen
5	chr4:110531600-110543800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr4:110531600-110543800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:110531600-110545000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:110531600-110546000	Weak transcription	Thymus	Thymus
9	chr4:110531600-110549600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:110531800-110543800	Weak transcription	Fetal Thymus	thymus
11	chr4:110532600-110545800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:110532800-110546000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:110533000-110573000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr4:110533400-110552800	Weak transcription	Primary B cells from cord blood	blood
15	chr4:110534400-110539600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr4:110534400-110539800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr4:110534800-110547000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr4:110536000-110545800	Weak transcription	Dnd41	blood
19	chr4:110536000-110552800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:110536200-110546000	Weak transcription	Aorta	Aorta
21	chr4:110536400-110538600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr4:110536400-110552800	Weak transcription	Adipose Nuclei	Adipose
23	chr4:110536400-110552800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:110537000-110538600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:110537000-110538600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr4:110537000-110539800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr4:110537200-110538600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:110537400-110538600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr4:110537400-110539400	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr4:110537400-110539400	Genic enhancers	Primary T cells from cord blood	blood
31	chr4:110537400-110543800	Weak transcription	Ovary	ovary
32	chr4:110537400-110547200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:110537600-110538800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr4:110538000-110538800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr4:110538000-110546000	Weak transcription	Gastric	stomach
36	chr4:110538200-110538600	Enhancers	H1 Cell Line	embryonic stem cell
37	chr4:110538200-110538600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr4:110538200-110538800	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr4:110538200-110539400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:110538400-110538600	Enhancers	GM12878-XiMat	blood
41	chr4:110538400-110539600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr4:110538400-110552000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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