Variant report

Variant	rs885654
Chromosome Location	chr3:119281590-119281591
allele	G/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	chr3:119281149-119281947	GM12878	blood:	n/a	n/a
2	TBL1XR1	chr3:119281162-119281922	GM12878	blood:	n/a	n/a
3	RELA	chr3:119281134-119281994	GM12891	blood:	n/a	chr3:119281542-119281551 chr3:119281542-119281551
4	POLR2A	chr3:119281115-119282025	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:119281118-119281991	GM19099	blood:	n/a	n/a
6	IRF4	chr3:119281132-119281830	GM12878	blood:	n/a	n/a
7	CUX1	chr3:119281301-119281933	GM12878	blood:	n/a	n/a
8	NFATC1	chr3:119281037-119282061	GM12878	blood:	n/a	n/a
9	CHD1	chr3:119280842-119281999	GM12878	blood:	n/a	n/a
10	TAF1	chr3:119281174-119281853	GM12878	blood:	n/a	n/a
11	NFIC	chr3:119280700-119282129	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:119281032-119282185	GM12892	blood:	n/a	n/a
13	YY1	chr3:119281172-119281610	GM12891	blood:	n/a	n/a
14	MAZ	chr3:119281140-119281942	GM12878	blood:	n/a	n/a
15	MXI1	chr3:119281134-119281996	GM12878	blood:	n/a	n/a
16	RELA	chr3:119281172-119281956	GM12892	blood:	n/a	chr3:119281542-119281551 chr3:119281542-119281551
17	RELA	chr3:119281155-119281944	GM10847	blood:	n/a	chr3:119281542-119281551 chr3:119281542-119281551
18	TAF1	chr3:119281154-119281873	GM12891	blood:	n/a	n/a
19	TCF12	chr3:119281298-119281847	GM12878	blood:	n/a	n/a
20	TAF1	chr3:119281158-119281860	GM12891	blood:	n/a	n/a
21	RELA	chr3:119281151-119281994	GM19099	blood:	n/a	chr3:119281542-119281551 chr3:119281542-119281551
22	SP1	chr3:119281148-119281952	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:119281130-119281950	Raji	blood:	n/a	n/a
24	YY1	chr3:119281211-119281939	GM12892	blood:	n/a	n/a
25	POLR2A	chr3:119280074-119282053	GM12891	blood:	n/a	n/a
26	POU2F2	chr3:119281153-119281925	GM12891	blood:	n/a	n/a
27	RCOR1	chr3:119281120-119281952	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:119281135-119281610	GM12878	blood:	n/a	n/a
29	IRF4	chr3:119281190-119281806	GM12878	blood:	n/a	n/a
30	YY1	chr3:119281117-119281927	GM12878	blood:	n/a	n/a
31	ATF2	chr3:119280942-119282102	GM12878	blood:	n/a	n/a
32	SP1	chr3:119281138-119281934	GM12878	blood:	n/a	n/a
33	STAT5A	chr3:119281028-119282096	GM12878	blood:	n/a	chr3:119281982-119281990
34	RFX5	chr3:119281113-119281826	GM12878	blood:	n/a	chr3:119281280-119281288 chr3:119281570-119281578
35	POLR2A	chr3:119281026-119282104	GM12892	blood:	n/a	n/a
36	BCL11A	chr3:119281169-119281949	GM12878	blood:	n/a	chr3:119281541-119281550
37	POLR2A	chr3:119281110-119281970	GM12878	blood:	n/a	n/a
38	MTA3	chr3:119281020-119282196	GM12878	blood:	n/a	n/a
39	EBF1	chr3:119281224-119281961	GM12878	blood:	n/a	n/a
40	BHLHE40	chr3:119281175-119281980	GM12878	blood:	n/a	n/a
41	PML	chr3:119279950-119282152	GM12878	blood:	n/a	chr3:119280307-119280315
42	POLR2A	chr3:119281116-119282043	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:119281101-119281888	GM19193	blood:	n/a	n/a
44	CREB1	chr3:119281102-119281994	GM12878	blood:	n/a	n/a
45	ZNF384	chr3:119281355-119281909	GM12878	blood:	n/a	n/a
46	RELA	chr3:119281160-119281874	GM18526	blood:	n/a	chr3:119281542-119281551 chr3:119281542-119281551
47	SMC3	chr3:119281209-119281936	GM12878	blood:	n/a	n/a
48	MEF2A	chr3:119281063-119281970	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:119281145-119281968	GM15510	blood:	n/a	n/a
50	NFIC	chr3:119280947-119282029	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119276600..119278656-chr3:119281431..119284119,2	K562	blood:
2	chr3:119276600..119278562-chr3:119281431..119283336,2	K562	blood:

Variant related genes	Relation type
CD80	TF binding region
ENSG00000121594	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10511393	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934494	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11533815	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11543525	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12487080	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487335	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487965	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489080	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492723	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494369	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494451	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12495673	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496129	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496841	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16829980	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16830002	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830004	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1852212	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019144	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2222630	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2222791	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34394661	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915165	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271391	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271393	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4330287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4407429	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55668872	0.90[EUR][1000 genomes]
rs55702208	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55738731	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55758148	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55772114	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55845727	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55848839	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55916342	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025972	0.87[EUR][1000 genomes]
rs56078908	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56086928	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56124423	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56135341	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56213221	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58613639	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58924738	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59223102	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59374417	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59529797	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59639276	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59701395	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59762006	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59764999	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59828023	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60920700	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61692996	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61702127	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66604554	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66797637	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66918189	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66920439	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67108211	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67160040	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67185025	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67212262	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67307954	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67369952	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67651191	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67765368	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68180496	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72953001	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73189896	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73189897	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73189899	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs762629	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762631	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867234	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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
5	nsv523837	chr3:119278848-119288848	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs885654	CD80	cis	Muscle Skeletal	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119267600-119298000	Weak transcription	Fetal Lung	lung
2	chr3:119278400-119282200	Enhancers	Primary B cells from peripheral blood	blood
3	chr3:119279200-119287400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:119280400-119281800	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr3:119280400-119282000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:119281200-119281600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:119281200-119281600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr3:119281200-119281600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:119281200-119281600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:119281200-119281600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:119281200-119281600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:119281200-119281600	Enhancers	Lung	lung
13	chr3:119281200-119281600	Enhancers	Pancreas	Pancrea
14	chr3:119281200-119281600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr3:119281200-119281600	Enhancers	Right Atrium	heart
16	chr3:119281200-119281600	Enhancers	Spleen	Spleen
17	chr3:119281200-119281800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:119281200-119281800	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr3:119281200-119281800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr3:119281200-119281800	Enhancers	Left Ventricle	heart
21	chr3:119281200-119281800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:119281200-119282000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr3:119281200-119282000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:119281200-119282000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:119281200-119282000	Flanking Active TSS	GM12878-XiMat	blood
26	chr3:119281400-119281600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:119281400-119281600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:119281400-119281600	Enhancers	Right Ventricle	heart
29	chr3:119281400-119281800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:119281400-119281800	Enhancers	Fetal Thymus	thymus

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