Variant report

Variant	rs56124423
Chromosome Location	chr3:119278163-119278164
allele	A/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	EBF1	chr3:119277828-119278760	GM12878	blood:	n/a	n/a
2	STAT5A	chr3:119278005-119278805	GM12878	blood:	n/a	n/a
3	ATF2	chr3:119277519-119278834	GM12878	blood:	n/a	n/a
4	RUNX3	chr3:119277645-119278297	GM12878	blood:	n/a	n/a
5	BCLAF1	chr3:119277506-119278857	GM12878	blood:	n/a	n/a
6	CTCF	chr3:119278080-119278230	GM12871	blood:	n/a	chr3:119278181-119278202
7	POLR2A	chr3:119277649-119279606	GM19099	blood:	n/a	n/a
8	BHLHE40	chr3:119277581-119278720	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:119277583-119279649	GM12891	blood:	n/a	n/a
10	ZNF143	chr3:119277717-119278776	GM12878	blood:	n/a	n/a
11	CTCF	chr3:119278011-119279041	GM12878	blood:	n/a	chr3:119278958-119278967 chr3:119278181-119278202 chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
12	PML	chr3:119277538-119279835	GM12878	blood:	n/a	n/a
13	YY1	chr3:119277651-119278589	GM12878	blood:	n/a	n/a
14	STAT3	chr3:119277801-119278809	GM12878	blood:	n/a	n/a
15	RELA	chr3:119277799-119279383	GM19099	blood:	n/a	n/a
16	NFIC	chr3:119277993-119278781	GM12878	blood:	n/a	n/a
17	STAT5A	chr3:119277527-119279616	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:119278157-119279235	GM18951	blood:	n/a	n/a
19	POLR2A	chr3:119277989-119279676	GM12892	blood:	n/a	n/a
20	BCLAF1	chr3:119278013-119279568	GM12878	blood:	n/a	n/a
21	FOXM1	chr3:119277650-119279476	GM12878	blood:	n/a	n/a
22	JUND	chr3:119277753-119278683	K562	blood:	n/a	n/a
23	MTA3	chr3:119277535-119279709	GM12878	blood:	n/a	n/a
24	CTCF	chr3:119278119-119278215	GM19240	blood:	n/a	chr3:119278181-119278202
25	MXI1	chr3:119277703-119278858	GM12878	blood:	n/a	n/a
26	RELA	chr3:119278040-119279439	GM18951	blood:	n/a	n/a
27	RCOR1	chr3:119277731-119278773	GM12878	blood:	n/a	n/a
28	RUNX3	chr3:119277625-119279563	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:119277630-119279599	GM18505	blood:	n/a	n/a
30	CHD1	chr3:119277633-119279564	GM12878	blood:	n/a	n/a
31	NFATC1	chr3:119277708-119279640	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:119278009-119279610	GM12892	blood:	n/a	n/a
33	CTCF	chr3:119278119-119278216	GM12892	blood:	n/a	chr3:119278181-119278202
34	BACH1	chr3:119278001-119278306	K562	blood:	n/a	n/a
35	POLR2A	chr3:119277531-119279675	GM12892	blood:	n/a	n/a
36	CCNT2	chr3:119278063-119278527	K562	blood:	n/a	n/a
37	TAF1	chr3:119278134-119278723	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:119277695-119279583	GM12892	blood:	n/a	n/a
39	RCOR1	chr3:119277775-119278761	K562	blood:	n/a	n/a
40	FOXM1	chr3:119277427-119278873	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:119278144-119279566	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:119277494-119279661	GM12892	blood:	n/a	n/a
43	CEBPB	chr3:119277982-119279063	GM12878	blood:	n/a	n/a
44	NFIC	chr3:119277612-119279873	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:119277232-119279740	GM12878	blood:	n/a	n/a
46	CTCF	chr3:119277983-119278971	A549	lung:	n/a	chr3:119278958-119278967 chr3:119278181-119278202 chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
47	SMC3	chr3:119277909-119278880	GM12878	blood:	n/a	chr3:119278514-119278528
48	WRNIP1	chr3:119277588-119279192	GM12878	blood:	n/a	n/a
49	RELA	chr3:119277730-119279557	GM15510	blood:	n/a	n/a
50	MAZ	chr3:119278045-119278751	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119218133..119220642-chr3:119277892..119280066,2	K562	blood:

Variant related genes	Relation type
CD80	TF binding region
ENSG00000113845	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10511393	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934494	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11533815	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11543525	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12487080	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487334	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487335	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487430	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487965	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489080	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492723	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494369	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494451	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12495673	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496129	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496520	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496841	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16829980	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829988	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16830002	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830004	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830008	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1852212	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019144	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2222630	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2222791	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34394661	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915165	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915166	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271391	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271393	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4330287	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4407429	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55668872	0.88[EUR][1000 genomes]
rs55702208	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55738731	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55758148	0.87[EUR][1000 genomes]
rs55772114	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55845727	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55848839	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55916342	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025972	0.85[EUR][1000 genomes]
rs56078908	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56086928	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56135341	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56213221	0.87[EUR][1000 genomes]
rs58613639	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58924738	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59223102	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59374417	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59529797	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59639276	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59701395	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59762006	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59764999	0.83[EUR][1000 genomes]
rs59828023	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60920700	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61692996	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61702127	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438537	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66604554	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66797637	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66918189	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66920439	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67108211	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67160040	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67185025	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67212262	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67307954	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67369952	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67651191	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67765368	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68180496	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72953001	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73189896	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73189897	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73189899	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs762629	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762631	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867234	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885654	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56124423	CD80	cis	Muscle Skeletal	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119267600-119298000	Weak transcription	Fetal Lung	lung
2	chr3:119271400-119281400	Weak transcription	Right Ventricle	heart
3	chr3:119275000-119278600	Weak transcription	Adipose Nuclei	Adipose
4	chr3:119275000-119278600	Weak transcription	Fetal Thymus	thymus
5	chr3:119275000-119281200	Weak transcription	Right Atrium	heart
6	chr3:119275000-119281200	Weak transcription	Spleen	Spleen
7	chr3:119275200-119278600	Active TSS	GM12878-XiMat	blood
8	chr3:119276600-119279200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr3:119276800-119278200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:119276800-119278200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:119277000-119281200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:119277600-119278200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr3:119277600-119278400	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr3:119277600-119278800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:119277600-119278800	Enhancers	Primary B cells from cord blood	blood
16	chr3:119277800-119278200	Active TSS	Primary T cells fromperipheralblood	blood
17	chr3:119277800-119278200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:119277800-119278400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:119277800-119278400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:119277800-119278400	Active TSS	Thymus	Thymus
21	chr3:119277800-119279200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr3:119278000-119278200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:119278000-119278200	Active TSS	K562	blood
24	chr3:119278000-119278200	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:119278000-119278400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:119278000-119278800	Enhancers	Primary hematopoietic stem cells	blood
27	chr3:119278000-119278800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:119278000-119278800	Active TSS	Rectal Mucosa Donor 29	rectum

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