Variant report

Variant	rs6533442
Chromosome Location	chr4:110553141-110553142
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1008327	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11728573	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11734973	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12513113	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13128388	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13846	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1543812	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17440077	0.90[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2158204	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2346835	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515508	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4698770	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698775	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62326054	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62326057	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62326058	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62327660	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533446	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6824270	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6824542	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6858416	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72674829	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7658262	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7690921	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6533442	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110533000-110573000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:110546000-110559600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr4:110546200-110566400	Weak transcription	Fetal Thymus	thymus
4	chr4:110546600-110580600	Weak transcription	Thymus	Thymus
5	chr4:110548000-110554200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr4:110548400-110553600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr4:110548600-110553800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:110550600-110569200	Weak transcription	GM12878-XiMat	blood
9	chr4:110550800-110553400	Genic enhancers	Primary T cells from cord blood	blood
10	chr4:110551400-110553400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr4:110551600-110553200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:110551800-110553200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:110552000-110553200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr4:110552000-110553400	Flanking Active TSS	A549	lung
15	chr4:110552000-110553600	Enhancers	Fetal Intestine Small	intestine
16	chr4:110552200-110553800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr4:110552600-110553200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr4:110552600-110553200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr4:110552600-110553200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:110552600-110553200	Enhancers	Fetal Intestine Large	intestine
21	chr4:110552600-110553400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr4:110552600-110553400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:110552800-110553200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:110552800-110553200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:110552800-110553200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr4:110552800-110553200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:110552800-110553200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:110552800-110553200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:110552800-110553200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr4:110552800-110553200	Enhancers	Primary B cells from cord blood	blood
31	chr4:110552800-110553200	Enhancers	Primary B cells from peripheral blood	blood
32	chr4:110552800-110553200	Enhancers	Primary T cells fromperipheralblood	blood
33	chr4:110552800-110553200	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr4:110552800-110553200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr4:110552800-110553200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr4:110552800-110553200	Enhancers	Adipose Nuclei	Adipose
37	chr4:110552800-110553200	Enhancers	Colon Smooth Muscle	Colon
38	chr4:110552800-110553200	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr4:110552800-110553200	Enhancers	Fetal Stomach	stomach
40	chr4:110552800-110553200	Enhancers	Ovary	ovary
41	chr4:110552800-110553200	Enhancers	Right Atrium	heart
42	chr4:110552800-110553200	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr4:110552800-110553400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr4:110552800-110553600	Enhancers	Fetal Brain Male	brain
45	chr4:110553000-110553200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr4:110553000-110565600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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