Variant report

Variant	rs1052080
Chromosome Location	chr4:73920622-73920623
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr4:73920589-73920779	H1-hESC	embryonic stem cell:	n/a	chr4:73920685-73920696
2	CEBPB	chr4:73920525-73920860	HepG2	liver:	n/a	chr4:73920685-73920696
3	CEBPB	chr4:73920538-73920874	A549	lung:	n/a	chr4:73920685-73920696
4	CEBPB	chr4:73920515-73920874	IMR90	lung:	n/a	chr4:73920685-73920696
5	POLR2A	chr4:73920554-73920754	GM12878	blood:	n/a	n/a
6	CEBPB	chr4:73920580-73920808	K562	blood:	n/a	chr4:73920685-73920696

No.	Distal block	Cell Line	Cell type
1	chr4:73916392..73919281-chr4:73919755..73922195,2	K562	blood:
2	chr4:73919886..73922171-chr4:73933999..73936377,2	MCF-7	breast:
3	chr4:73919855..73921489-chr4:73934521..73936541,2	K562	blood:
4	chr4:73913250..73915803-chr4:73919597..73921645,2	K562	blood:
5	chr4:73918831..73921818-chr4:73928688..73931173,2	K562	blood:
6	chr4:73918845..73921259-chr4:74116403..74118681,2	MCF-7	breast:
7	chr4:73919855..73923746-chr4:73932924..73936555,4	K562	blood:

Variant related genes	Relation type
ENSG00000272859	TF binding region
ENSG00000272859	Chromatin interaction
ENSG00000163626	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11721329	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727957	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11929937	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12500051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12507846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13107336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13135799	0.84[ASN][1000 genomes]
rs13149759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13151642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17178078	0.85[ASN][1000 genomes]
rs1996057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs34230856	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34716955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62309635	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67424539	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6855349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7442235	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973541	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949371	chr4:73678470-74094500	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv432611	chr4:73740665-74099265	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv523169	chr4:73752242-74120910	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv998707	chr4:73753922-74044843	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv537136	chr4:73753922-74044843	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv917017	chr4:73754127-74044830	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1013174	chr4:73785324-74031884	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv537137	chr4:73785324-74031884	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1012068	chr4:73817769-74003079	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv1014088	chr4:73817769-74031884	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv537138	chr4:73817769-74031884	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv533502	chr4:73819067-74044813	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1052080	COX18	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:73911000-73922600	Weak transcription	Spleen	Spleen
2	chr4:73911400-73924600	Weak transcription	Pancreas	Pancrea
3	chr4:73912600-73922000	Weak transcription	Aorta	Aorta
4	chr4:73915200-73922800	Weak transcription	Right Ventricle	heart
5	chr4:73915200-73925600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:73916200-73921000	Weak transcription	NH-A	brain
7	chr4:73916200-73921400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:73916200-73924400	Weak transcription	A549	lung
9	chr4:73917000-73922000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:73917200-73923800	Weak transcription	Gastric	stomach
11	chr4:73917200-73931000	Weak transcription	Fetal Heart	heart
12	chr4:73917200-73933800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:73917400-73921200	Weak transcription	Fetal Lung	lung
14	chr4:73917400-73922600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:73917400-73932000	Weak transcription	Psoas Muscle	Psoas
16	chr4:73917600-73920800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr4:73917600-73921000	Weak transcription	Left Ventricle	heart
18	chr4:73917600-73921400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:73917600-73921600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr4:73917600-73921600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr4:73917600-73922600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:73917600-73923800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:73917800-73920800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:73917800-73921000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:73917800-73921000	Weak transcription	Fetal Brain Female	brain
26	chr4:73917800-73921600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:73917800-73921800	Weak transcription	HSMMtube	muscle
28	chr4:73917800-73923400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:73917800-73924600	Weak transcription	Esophagus	oesophagus
30	chr4:73918000-73920800	Weak transcription	Dnd41	blood
31	chr4:73918000-73921400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr4:73918000-73924600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:73918000-73924800	Weak transcription	NHEK	skin
34	chr4:73918200-73920800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:73918200-73920800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:73918400-73921200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:73918400-73922600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:73918400-73922600	Weak transcription	Fetal Intestine Small	intestine
39	chr4:73918400-73922600	Weak transcription	Fetal Stomach	stomach
40	chr4:73918600-73921600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr4:73918600-73933000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr4:73918800-73921600	Enhancers	H1 Cell Line	embryonic stem cell
43	chr4:73918800-73921600	Strong transcription	Primary T cells from cord blood	blood
44	chr4:73918800-73930200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr4:73918800-73932200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:73918800-73933400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:73919000-73921200	Weak transcription	HepG2	liver
48	chr4:73919000-73926000	Strong transcription	Thymus	Thymus
49	chr4:73919000-73928600	Strong transcription	Fetal Intestine Large	intestine
50	chr4:73919000-73931400	Strong transcription	Liver	Liver

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