Variant report

Variant	rs4722551
Chromosome Location	chr7:25991826-25991827
allele	C/T
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	USF1	chr7:25991690-25991938	HepG2	liver:	n/a	n/a
2	MAX	chr7:25991623-25991944	H1-hESC	embryonic stem cell:	n/a	chr7:25991807-25991816 chr7:25991805-25991818 chr7:25991806-25991817 chr7:25991807-25991816 chr7:25991805-25991818
3	BHLHE40	chr7:25991654-25992753	HepG2	liver:	n/a	n/a
4	MYC	chr7:25991688-25991983	H1-hESC	embryonic stem cell:	n/a	chr7:25991807-25991816 chr7:25991805-25991818 chr7:25991806-25991817 chr7:25991807-25991816 chr7:25991805-25991818
5	POLR2A	chr7:25987021-25992694	HepG2	liver:	n/a	n/a
6	USF2	chr7:25991644-25991931	HepG2	liver:	n/a	n/a
7	USF2	chr7:25991592-25991982	H1-hESC	embryonic stem cell:	n/a	n/a
8	USF1	chr7:25991578-25992023	H1-hESC	embryonic stem cell:	n/a	n/a
9	USF1	chr7:25991553-25991944	HepG2	liver:	n/a	n/a
10	USF2	chr7:25991631-25991960	GM12878	blood:	n/a	n/a
11	MAX	chr7:25990769-25991971	H1-hESC	embryonic stem cell:	n/a	chr7:25990932-25990943 chr7:25991249-25991259 chr7:25991807-25991816 chr7:25991805-25991818 chr7:25991806-25991817 chr7:25991807-25991816 chr7:25991805-25991818
12	POLR2A	chr7:25991583-25991921	H1-hESC	embryonic stem cell:	n/a	n/a
13	USF1	chr7:25991615-25991966	K562	blood:	n/a	n/a
14	USF1	chr7:25991513-25992061	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr7:25989186-25991998	H1-hESC	embryonic stem cell:	n/a	n/a
16	E2F6	chr7:25991049-25992052	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr7:25991598-25992011	H1-hESC	embryonic stem cell:	n/a	chr7:25991807-25991816 chr7:25991805-25991818 chr7:25991806-25991817 chr7:25991807-25991816 chr7:25991805-25991818

No.	Distal block	Cell Line	Cell type
1	chr7:25932775..25935474-chr7:25989853..25992220,2	K562	blood:
2	chr11:128392124..128392882-chr7:25991162..25992153,2	HCT-116	colon:
3	chr7:25932084..25934727-chr7:25991166..25992811,2	MCF-7	breast:
4	chr7:25990509..25992566-chr7:25994471..25996898,2	K562	blood:
5	chr7:25990207..25991830-chr7:26094178..26097069,2	MCF-7	breast:
6	chr7:25965773..25968588-chr7:25989969..25992378,2	MCF-7	breast:
7	chr7:25990038..25992521-chr7:26240210..26242861,2	MCF-7	breast:
8	chr7:25990295..25993400-chr7:26020103..26023231,3	MCF-7	breast:
9	chr7:25990769..25992627-chr7:25993165..25995306,2	MCF-7	breast:
10	chr7:25990709..25992651-chr7:26072086..26075062,2	MCF-7	breast:
11	chr7:25989265..25991851-chr7:26238825..26240746,4	MCF-7	breast:
12	chr7:25901871..25903514-chr7:25989852..25991943,2	K562	blood:
13	chr7:25989811..25992726-chr7:26096097..26097704,2	MCF-7	breast:
14	chr7:25901385..25904121-chr7:25989908..25991928,2	MCF-7	breast:
15	chr7:25990548..25994647-chr7:26001939..26005377,4	MCF-7	breast:
16	chr7:25952760..25954350-chr7:25989892..25992459,2	K562	blood:
17	chr7:25990246..25992488-chr7:26100564..26102799,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270933	TF binding region
MIR148A	TF binding region
ENSG00000134954	Chromatin interaction
ENSG00000122566	Chromatin interaction
ENSG00000122565	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11760762	0.93[ASN][1000 genomes]
rs12700679	0.93[ASN][1000 genomes]
rs12700680	0.93[ASN][1000 genomes]
rs12700681	0.93[ASN][1000 genomes]
rs12700682	0.93[ASN][1000 genomes]
rs13226851	0.93[ASN][1000 genomes]
rs13231897	0.93[ASN][1000 genomes]
rs17729097	0.93[ASN][1000 genomes]
rs2391175	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs35336240	0.93[ASN][1000 genomes]
rs4236321	0.83[CHD][hapmap];0.93[ASN][1000 genomes]
rs4412274	0.93[ASN][1000 genomes]
rs4422683	0.93[ASN][1000 genomes]
rs4640955	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs4722545	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs4722546	0.93[ASN][1000 genomes]
rs4722547	0.93[ASN][1000 genomes]
rs4722548	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs66700050	0.93[ASN][1000 genomes]
rs67494041	0.93[ASN][1000 genomes]
rs6963094	1.00[CHB][hapmap]
rs6977848	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs735316	0.93[ASN][1000 genomes]
rs7810017	0.93[ASN][1000 genomes]
rs997988	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv606432	chr7:25988185-26223294	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	esv3394736	chr7:25989527-25992275	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	90 gene(s)	inside rSNPs	diseases
5	esv3425784	chr7:25989652-25992200	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:3)

Disease	PMID	Source
LDL cholesterol	24097068	GWAS catalog
Cholesterol, total	24097068	GWAS catalog
Triglycerides	24097068	GWAS catalog

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25987200-25993200	Active TSS	Pancreas	Pancrea
2	chr7:25987800-25992800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr7:25989200-25992600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr7:25989400-25992000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:25989400-25992400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr7:25989600-25992000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr7:25989600-25992000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr7:25990000-25992000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:25990400-25992200	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr7:25990800-25992000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:25990800-25992000	Enhancers	Spleen	Spleen
12	chr7:25991200-25992000	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr7:25991200-25992000	Flanking Active TSS	HMEC	breast
14	chr7:25991200-25993200	Flanking Active TSS	Liver	Liver
15	chr7:25991400-25992000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr7:25991400-25992000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr7:25991400-25992800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr7:25991400-25993000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr7:25991400-25993200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr7:25991600-25992000	Enhancers	Primary hematopoietic stem cells	blood
21	chr7:25991600-25992000	Flanking Active TSS	Fetal Intestine Small	intestine
22	chr7:25991600-25992000	Flanking Active TSS	Stomach Mucosa	stomach
23	chr7:25991600-25992400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:25991600-25992600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr7:25991600-25994000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:25991800-25992000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:25991800-25992000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:25991800-25992000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr7:25991800-25992000	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr7:25991800-25992000	Enhancers	Stomach Smooth Muscle	stomach
31	chr7:25991800-25992000	Active TSS	NHDF-Ad	bronchial
32	chr7:25991800-25992400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:25991800-25992400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:25991800-25992400	Weak transcription	Fetal Kidney	kidney
35	chr7:25991800-25992400	Active TSS	HepG2	liver
36	chr7:25991800-25992600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr7:25991800-25992600	Enhancers	Fetal Intestine Large	intestine
38	chr7:25991800-25992800	Enhancers	H1 Cell Line	embryonic stem cell
39	chr7:25991800-25992800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr7:25991800-25992800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr7:25991800-25992800	Active TSS	Duodenum Mucosa	Duodenum
42	chr7:25991800-25993000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:25991800-25993000	Weak transcription	GM12878-XiMat	blood

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