Variant report

Variant	rs26680
Chromosome Location	chr5:52284386-52284387
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	POLR2A	chr5:52284380-52286686	HepG2	liver:	n/a	n/a
2	PBX3	chr5:52283236-52284404	SK-N-SH	brain:	n/a	n/a
3	ARID3A	chr5:52283768-52284583	HepG2	liver:	n/a	n/a
4	FOS	chr5:52283422-52284604	MCF10A-Er-Src	breast:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
5	SP1	chr5:52284361-52285479	A549	lung:	n/a	chr5:52284859-52284868 chr5:52284858-52284870 chr5:52284858-52284870 chr5:52284859-52284869
6	POLR2A	chr5:52283218-52289712	MCF10A-Er-Src	breast:	n/a	n/a
7	MAX	chr5:52284380-52286140	A549	lung:	n/a	n/a
8	FOS	chr5:52283341-52284547	HUVEC	blood vessel:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
9	GATA3	chr5:52283281-52284417	MCF-7	breast:	n/a	chr5:52283859-52283870 chr5:52283852-52283862 chr5:52283975-52283988 chr5:52283849-52283865
10	POLR2A	chr5:52283457-52286738	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr5:52283273-52285404	HUVEC	blood vessel:	n/a	n/a
12	MAX	chr5:52283269-52286257	HCT-116	colon:	n/a	n/a
13	SMC3	chr5:52283431-52286639	Hela-S3	cervix:	n/a	chr5:52284958-52284968 chr5:52286518-52286525 chr5:52284773-52284783 chr5:52285498-52285505
14	POLR2A	chr5:52283657-52284636	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr5:52283340-52286348	Hela-S3	cervix:	n/a	n/a
16	TCF12	chr5:52283214-52286357	SK-N-SH	brain:	n/a	chr5:52285000-52285007
17	EGR1	chr5:52284368-52285841	HCT-116	colon:	n/a	chr5:52284854-52284867 chr5:52284856-52284866 chr5:52284856-52284866 chr5:52284853-52284868 chr5:52284855-52284866 chr5:52284857-52284866 chr5:52284857-52284867 chr5:52284854-52284867 chr5:52284854-52284867 chr5:52284854-52284867 chr5:52284854-52284868
18	POLR2A	chr5:52284242-52284534	HCT-116	colon:	n/a	n/a
19	POLR2A	chr5:52284355-52285538	PANC-1	pancreas:	n/a	n/a
20	GATA3	chr5:52283181-52284453	SK-N-SH	brain:	n/a	chr5:52283859-52283870 chr5:52283852-52283862 chr5:52283975-52283988 chr5:52283849-52283865
21	STAT3	chr5:52283449-52284502	Hela-S3	cervix:	n/a	chr5:52283552-52283560 chr5:52283676-52283683
22	POLR2A	chr5:52284297-52286391	HUVEC	blood vessel:	n/a	n/a
23	RCOR1	chr5:52283365-52286319	Hela-S3	cervix:	n/a	n/a
24	GATA3	chr5:52283137-52286400	SK-N-SH	brain:	n/a	chr5:52283859-52283870 chr5:52283852-52283862 chr5:52286193-52286203 chr5:52283975-52283988 chr5:52285535-52285545 chr5:52283849-52283865
25	POLR2A	chr5:52284317-52285868	HepG2	liver:	n/a	n/a
26	POLR2A	chr5:52283338-52284617	SK-N-SH	brain:	n/a	n/a
27	TCF7L2	chr5:52283442-52284461	PANC-1	pancreas:	n/a	chr5:52283895-52283904 chr5:52283896-52283903
28	POLR2A	chr5:52284296-52284641	HepG2	liver:	n/a	n/a
29	SMARCC1	chr5:52283300-52286263	Hela-S3	cervix:	n/a	chr5:52283627-52283636
30	STAT3	chr5:52283201-52284745	MCF10A-Er-Src	breast:	n/a	chr5:52283552-52283560 chr5:52283676-52283683
31	NFIC	chr5:52283258-52284419	SK-N-SH	brain:	n/a	n/a
32	HEY1	chr5:52284102-52284702	HepG2	liver:	n/a	n/a
33	MXI1	chr5:52284162-52286490	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:52277482..52279538-chr5:52282210..52284601,2	K562	blood:
2	chr5:52243208..52246085-chr5:52282017..52284486,2	MCF-7	breast:
3	chr5:52282064..52285632-chr5:52404082..52406997,3	MCF-7	breast:
4	chr5:52282372..52286768-chr5:52384365..52386788,6	MCF-7	breast:

Variant related genes	Relation type
ITGA2	TF binding region
ENSG00000272123	Chromatin interaction
ENSG00000247796	Chromatin interaction
ENSG00000164172	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12517213	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1645761	1.00[CEU][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs190310	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2264397	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2279584	0.84[MEX][hapmap]
rs2432230	0.94[EUR][1000 genomes]
rs26679	0.81[LWK][hapmap]
rs27618	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs33444	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35236	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs397808	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs462383	0.81[AFR][1000 genomes];0.84[EUR][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	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs26680	ITGA2	cis	multi-tissue	Pritchard
rs26680	MOCS2	cis	cerebellum	SCAN
rs26680	PARP8	cis	cerebellum	SCAN
rs26680	ISL1	cis	parietal	SCAN
rs26680	ITGA2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52282600-52284400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr5:52282800-52284600	Weak transcription	Lung	lung
3	chr5:52283200-52284400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:52283200-52284400	Enhancers	Duodenum Mucosa	Duodenum
5	chr5:52283200-52284400	Enhancers	Fetal Intestine Large	intestine
6	chr5:52283200-52284400	Enhancers	Fetal Intestine Small	intestine
7	chr5:52283200-52284400	Enhancers	NHLF	lung
8	chr5:52283200-52284600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr5:52283200-52284600	Enhancers	Osteobl	bone
10	chr5:52283200-52284800	Flanking Active TSS	Hela-S3	cervix
11	chr5:52283400-52284400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr5:52283400-52284400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:52283400-52284400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:52283400-52284600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:52283400-52284600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:52283400-52284600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:52283400-52284600	Enhancers	Stomach Mucosa	stomach
18	chr5:52283400-52284600	Flanking Active TSS	A549	lung
19	chr5:52283400-52285000	Flanking Active TSS	HMEC	breast
20	chr5:52283400-52285000	Flanking Active TSS	HUVEC	blood vessel
21	chr5:52283600-52284400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:52283600-52284400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:52283600-52284600	Flanking Active TSS	HepG2	liver
24	chr5:52283800-52284400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:52283800-52284400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:52283800-52284400	Enhancers	Fetal Kidney	kidney
27	chr5:52283800-52284400	Enhancers	NH-A	brain
28	chr5:52283800-52284600	Weak transcription	Psoas Muscle	Psoas
29	chr5:52284000-52284400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:52284000-52284400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:52284000-52284400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:52284000-52284600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:52284000-52284600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr5:52284000-52284600	Bivalent Enhancer	Dnd41	blood
35	chr5:52284000-52284800	Flanking Active TSS	NHEK	skin
36	chr5:52284000-52288000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr5:52284200-52284400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
38	chr5:52284200-52284400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:52284200-52284400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:52284200-52284400	Bivalent Enhancer	Brain Hippocampus Middle	brain
41	chr5:52284200-52284400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr5:52284200-52284400	Enhancers	Right Ventricle	heart
43	chr5:52284200-52284400	Enhancers	NHDF-Ad	bronchial
44	chr5:52284200-52284600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:52284200-52284600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
46	chr5:52284200-52285400	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr5:52284200-52286400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr5:52284200-52286600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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