Variant report

Variant	rs26679
Chromosome Location	chr5:52284175-52284176
allele	C/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	GATA3	chr5:52283212-52284288	A549	lung:	n/a	chr5:52283859-52283870 chr5:52283852-52283862 chr5:52283975-52283988 chr5:52283849-52283865
2	SIN3AK20	chr5:52283306-52284268	HCT-116	colon:	n/a	n/a
3	PBX3	chr5:52283324-52284303	SK-N-SH	brain:	n/a	n/a
4	JUND	chr5:52283224-52284268	SK-N-SH	brain:	n/a	chr5:52283904-52283915 chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
5	MAFK	chr5:52283480-52284316	Hela-S3	cervix:	n/a	chr5:52283568-52283583
6	PBX3	chr5:52283236-52284404	SK-N-SH	brain:	n/a	n/a
7	TEAD4	chr5:52283307-52284189	SK-N-SH	brain:	n/a	n/a
8	TEAD4	chr5:52283365-52284280	HCT-116	colon:	n/a	n/a
9	ARID3A	chr5:52283768-52284583	HepG2	liver:	n/a	n/a
10	SIN3AK20	chr5:52283241-52284254	MCF-7	breast:	n/a	n/a
11	FOSL1	chr5:52283122-52284359	HCT-116	colon:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
12	FOS	chr5:52283422-52284604	MCF10A-Er-Src	breast:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
13	NR2F2	chr5:52283388-52284227	MCF-7	breast:	n/a	n/a
14	POLR2A	chr5:52283218-52289712	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr5:52283186-52284329	HUVEC	blood vessel:	n/a	n/a
16	MYC	chr5:52283452-52284178	MCF10A-Er-Src	breast:	n/a	n/a
17	MAX	chr5:52283377-52284175	HCT-116	colon:	n/a	n/a
18	POLR2A	chr5:52283853-52284237	Hela-S3	cervix:	n/a	n/a
19	FOS	chr5:52283341-52284547	HUVEC	blood vessel:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
20	GATA3	chr5:52283281-52284417	MCF-7	breast:	n/a	chr5:52283859-52283870 chr5:52283852-52283862 chr5:52283975-52283988 chr5:52283849-52283865
21	TCF12	chr5:52283361-52284257	A549	lung:	n/a	n/a
22	GATA2	chr5:52283340-52284220	HUVEC	blood vessel:	n/a	chr5:52283859-52283870 chr5:52283852-52283862 chr5:52283975-52283988 chr5:52283849-52283865
23	POLR2A	chr5:52283457-52286738	Hela-S3	cervix:	n/a	n/a
24	JUND	chr5:52283248-52284294	HCT-116	colon:	n/a	chr5:52283904-52283915 chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
25	POLR2A	chr5:52283273-52285404	HUVEC	blood vessel:	n/a	n/a
26	MAX	chr5:52283269-52286257	HCT-116	colon:	n/a	n/a
27	SMC3	chr5:52283431-52286639	Hela-S3	cervix:	n/a	chr5:52284958-52284968 chr5:52286518-52286525 chr5:52284773-52284783 chr5:52285498-52285505
28	EP300	chr5:52283179-52284363	SK-N-SH	brain:	n/a	chr5:52283269-52283278
29	FOSL2	chr5:52283357-52284376	SK-N-SH	brain:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
30	POLR2A	chr5:52283657-52284636	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr5:52283340-52286348	Hela-S3	cervix:	n/a	n/a
32	TCF12	chr5:52283214-52286357	SK-N-SH	brain:	n/a	chr5:52285000-52285007
33	RFX5	chr5:52283442-52284195	Hela-S3	cervix:	n/a	n/a
34	TEAD4	chr5:52283194-52284379	SK-N-SH	brain:	n/a	n/a
35	JUND	chr5:52283387-52284345	SK-N-SH	brain:	n/a	chr5:52283904-52283915 chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
36	GATA3	chr5:52283181-52284453	SK-N-SH	brain:	n/a	chr5:52283859-52283870 chr5:52283852-52283862 chr5:52283975-52283988 chr5:52283849-52283865
37	SRF	chr5:52283337-52284336	HCT-116	colon:	n/a	n/a
38	FOSL1	chr5:52283267-52284252	HCT-116	colon:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
39	TCF12	chr5:52283222-52284275	SK-N-SH	brain:	n/a	n/a
40	FOSL2	chr5:52283297-52284263	A549	lung:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
41	SP1	chr5:52283226-52284284	HCT-116	colon:	n/a	chr5:52283528-52283538 chr5:52283529-52283538 chr5:52283528-52283542
42	MAZ	chr5:52283403-52284320	Hela-S3	cervix:	n/a	n/a
43	STAT3	chr5:52283449-52284502	Hela-S3	cervix:	n/a	chr5:52283552-52283560 chr5:52283676-52283683
44	STAT3	chr5:52283433-52284185	MCF10A-Er-Src	breast:	n/a	chr5:52283552-52283560 chr5:52283676-52283683
45	RCOR1	chr5:52283365-52286319	Hela-S3	cervix:	n/a	n/a
46	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
47	GATA3	chr5:52283338-52284299	MCF-7	breast:	n/a	chr5:52283859-52283870 chr5:52283852-52283862 chr5:52283975-52283988 chr5:52283849-52283865
48	POLR2A	chr5:52283338-52284617	SK-N-SH	brain:	n/a	n/a
49	SP1	chr5:52283176-52284321	HCT-116	colon:	n/a	chr5:52283528-52283538 chr5:52283529-52283538 chr5:52283528-52283542
50	BRCA1	chr5:52283486-52284226	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:52278874..52281430-chr5:52281937..52284347,4	MCF-7	breast:
2	chr5:52277482..52279538-chr5:52282210..52284601,2	K562	blood:
3	chr5:52243208..52246085-chr5:52282017..52284486,2	MCF-7	breast:
4	chr5:52282064..52285632-chr5:52404082..52406997,3	MCF-7	breast:
5	chr5:52282372..52286768-chr5:52384365..52386788,6	MCF-7	breast:

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

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs26680	0.81[LWK][hapmap]
rs26681	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28095	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33447	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33448	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42776	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861460	0.89[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs26679	PARP8	cis	cerebellum	SCAN
rs26679	ITGA2	cis	parietal	SCAN
rs26679	ITGA2	cis	Adipose Subcutaneous	GTEx
rs26679	ITGA2	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52279200-52284200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:52282600-52284400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:52282800-52284600	Weak transcription	Lung	lung
4	chr5:52283200-52284400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:52283200-52284400	Enhancers	Duodenum Mucosa	Duodenum
6	chr5:52283200-52284400	Enhancers	Fetal Intestine Large	intestine
7	chr5:52283200-52284400	Enhancers	Fetal Intestine Small	intestine
8	chr5:52283200-52284400	Enhancers	NHLF	lung
9	chr5:52283200-52284600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:52283200-52284600	Enhancers	Osteobl	bone
11	chr5:52283200-52284800	Flanking Active TSS	Hela-S3	cervix
12	chr5:52283400-52284400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr5:52283400-52284400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:52283400-52284400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:52283400-52284600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:52283400-52284600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:52283400-52284600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:52283400-52284600	Enhancers	Stomach Mucosa	stomach
19	chr5:52283400-52284600	Flanking Active TSS	A549	lung
20	chr5:52283400-52285000	Flanking Active TSS	HMEC	breast
21	chr5:52283400-52285000	Flanking Active TSS	HUVEC	blood vessel
22	chr5:52283600-52284400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:52283600-52284400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:52283600-52284600	Flanking Active TSS	HepG2	liver
25	chr5:52283800-52284200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:52283800-52284400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:52283800-52284400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:52283800-52284400	Enhancers	Fetal Kidney	kidney
29	chr5:52283800-52284400	Enhancers	NH-A	brain
30	chr5:52283800-52284600	Weak transcription	Psoas Muscle	Psoas
31	chr5:52284000-52284200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
32	chr5:52284000-52284200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:52284000-52284200	Enhancers	Brain Cingulate Gyrus	brain
34	chr5:52284000-52284200	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr5:52284000-52284200	Enhancers	Small Intestine	intestine
36	chr5:52284000-52284200	Flanking Active TSS	NHDF-Ad	bronchial
37	chr5:52284000-52284400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:52284000-52284400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:52284000-52284400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:52284000-52284600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:52284000-52284600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr5:52284000-52284600	Bivalent Enhancer	Dnd41	blood
43	chr5:52284000-52284800	Flanking Active TSS	NHEK	skin
44	chr5:52284000-52288000	Active TSS	Breast Myoepithelial Primary Cells	Breast

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