Variant report

Variant	rs3212383
Chromosome Location	chr5:52283961-52283962
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	GATA3	chr5:52283212-52284288	A549	lung:	n/a	chr5:52283859-52283870 chr5:52283852-52283862 chr5:52283975-52283988 chr5:52283849-52283865
2	GABPA	chr5:52283493-52283993	A549	lung:	n/a	n/a
3	SIN3AK20	chr5:52283306-52284268	HCT-116	colon:	n/a	n/a
4	FOSL2	chr5:52283615-52284056	HepG2	liver:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
5	RAD21	chr5:52283412-52284104	Hela-S3	cervix:	n/a	n/a
6	TEAD4	chr5:52283331-52284140	HCT-116	colon:	n/a	n/a
7	SP1	chr5:52283234-52284018	A549	lung:	n/a	chr5:52283528-52283538 chr5:52283529-52283538 chr5:52283528-52283542
8	FOS	chr5:52283443-52284128	Hela-S3	cervix:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
9	PBX3	chr5:52283324-52284303	SK-N-SH	brain:	n/a	n/a
10	RXRA	chr5:52283312-52284174	SK-N-SH	brain:	n/a	chr5:52283893-52283906 chr5:52283893-52283906 chr5:52283890-52283910 chr5:52283893-52283906
11	JUND	chr5:52283224-52284268	SK-N-SH	brain:	n/a	chr5:52283904-52283915 chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
12	MAFK	chr5:52283480-52284316	Hela-S3	cervix:	n/a	chr5:52283568-52283583
13	PBX3	chr5:52283236-52284404	SK-N-SH	brain:	n/a	n/a
14	CHD2	chr5:52283347-52284122	Hela-S3	cervix:	n/a	n/a
15	TEAD4	chr5:52283307-52284189	SK-N-SH	brain:	n/a	n/a
16	TEAD4	chr5:52283365-52284280	HCT-116	colon:	n/a	n/a
17	ARID3A	chr5:52283768-52284583	HepG2	liver:	n/a	n/a
18	SIN3AK20	chr5:52283241-52284254	MCF-7	breast:	n/a	n/a
19	FOS	chr5:52283451-52284110	MCF10A-Er-Src	breast:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
20	FOSL1	chr5:52283122-52284359	HCT-116	colon:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
21	FOS	chr5:52283422-52284604	MCF10A-Er-Src	breast:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
22	RXRA	chr5:52283369-52284049	SK-N-SH	brain:	n/a	chr5:52283893-52283906 chr5:52283893-52283906 chr5:52283890-52283910 chr5:52283893-52283906
23	NR2F2	chr5:52283388-52284227	MCF-7	breast:	n/a	n/a
24	POLR2A	chr5:52283218-52289712	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr5:52283186-52284329	HUVEC	blood vessel:	n/a	n/a
26	ZNF217	chr5:52283397-52284083	MCF-7	breast:	n/a	n/a
27	EP300	chr5:52283655-52284047	HepG2	liver:	n/a	n/a
28	MYC	chr5:52283452-52284178	MCF10A-Er-Src	breast:	n/a	n/a
29	MYC	chr5:52283453-52284091	MCF10A-Er-Src	breast:	n/a	n/a
30	MAX	chr5:52283377-52284175	HCT-116	colon:	n/a	n/a
31	MXI1	chr5:52283435-52284111	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr5:52283853-52284237	Hela-S3	cervix:	n/a	n/a
33	FOS	chr5:52283341-52284547	HUVEC	blood vessel:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
34	GATA3	chr5:52283281-52284417	MCF-7	breast:	n/a	chr5:52283859-52283870 chr5:52283852-52283862 chr5:52283975-52283988 chr5:52283849-52283865
35	JUND	chr5:52283421-52284152	MCF-7	breast:	n/a	chr5:52283904-52283915 chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
36	STAT3	chr5:52283366-52284098	MCF10A-Er-Src	breast:	n/a	chr5:52283552-52283560 chr5:52283676-52283683
37	TCF12	chr5:52283361-52284257	A549	lung:	n/a	n/a
38	GATA2	chr5:52283340-52284220	HUVEC	blood vessel:	n/a	chr5:52283859-52283870 chr5:52283852-52283862 chr5:52283975-52283988 chr5:52283849-52283865
39	POLR2A	chr5:52283457-52286738	Hela-S3	cervix:	n/a	n/a
40	JUND	chr5:52283248-52284294	HCT-116	colon:	n/a	chr5:52283904-52283915 chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636
41	POLR2A	chr5:52283273-52285404	HUVEC	blood vessel:	n/a	n/a
42	SP1	chr5:52283328-52284126	A549	lung:	n/a	chr5:52283528-52283538 chr5:52283529-52283538 chr5:52283528-52283542
43	USF2	chr5:52283502-52284103	Hela-S3	cervix:	n/a	n/a
44	MAX	chr5:52283269-52286257	HCT-116	colon:	n/a	n/a
45	EP300	chr5:52283346-52284119	SK-N-SH	brain:	n/a	n/a
46	SMC3	chr5:52283431-52286639	Hela-S3	cervix:	n/a	chr5:52284958-52284968 chr5:52286518-52286525 chr5:52284773-52284783 chr5:52285498-52285505
47	TCF7L2	chr5:52283418-52284169	Hela-S3	cervix:	n/a	chr5:52283895-52283904 chr5:52283896-52283903
48	SIN3AK20	chr5:52283348-52284157	HCT-116	colon:	n/a	n/a
49	GABPA	chr5:52283435-52283974	MCF-7	breast:	n/a	n/a
50	FOSL2	chr5:52283320-52284066	MCF-7	breast:	n/a	chr5:52283626-52283638 chr5:52283631-52283643 chr5:52283628-52283636

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
ENSG00000164172	Chromatin interaction
ENSG00000272123	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10513004	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs10940280	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs11738606	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11739571	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11742694	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11742813	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11748504	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11749081	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12186544	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13156420	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13165509	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13179969	0.91[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs13180488	0.85[EUR][1000 genomes]
rs1421943	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1592795	0.81[EUR][1000 genomes]
rs3212414	0.81[EUR][1000 genomes]
rs3212656	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34288275	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34352729	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34512129	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34865297	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35597318	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35657730	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35862618	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35926366	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4865755	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6859171	1.00[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs7702766	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7713782	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9791046	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3212383	ITGA2	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

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

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