Variant report

Variant	rs41271393
Chromosome Location	chr3:119278693-119278694
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	chr3:119278283-119279546	Raji	blood:	n/a	n/a
2	POLR2A	chr3:119278320-119279538	GM12878	blood:	n/a	n/a
3	EBF1	chr3:119277828-119278760	GM12878	blood:	n/a	n/a
4	RAD21	chr3:119278282-119278698	H1-hESC	embryonic stem cell:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
5	ZMIZ1	chr3:119278447-119278703	K562	blood:	n/a	n/a
6	RAD21	chr3:119278217-119278791	H1-hESC	embryonic stem cell:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
7	RAD21	chr3:119278303-119278785	MCF-7	breast:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
8	CTCF	chr3:119278389-119278721	GM19240	blood:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
9	EP300	chr3:119278335-119278696	GM12878	blood:	n/a	chr3:119278387-119278401
10	STAT5A	chr3:119278005-119278805	GM12878	blood:	n/a	n/a
11	ATF2	chr3:119277519-119278834	GM12878	blood:	n/a	n/a
12	POU2F2	chr3:119278263-119278900	GM12878	blood:	n/a	chr3:119278515-119278527 chr3:119278584-119278596
13	SMC3	chr3:119278332-119278698	K562	blood:	n/a	chr3:119278514-119278528
14	PML	chr3:119278245-119278731	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:119278185-119279438	GM15510	blood:	n/a	n/a
16	TBL1XR1	chr3:119278218-119278720	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:119278609-119278748	K562	blood:	n/a	n/a
18	MAX	chr3:119278325-119278693	K562	blood:	n/a	n/a
19	RAD21	chr3:119278346-119278727	GM12878	blood:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
20	BCLAF1	chr3:119277506-119278857	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:119277649-119279606	GM19099	blood:	n/a	n/a
22	CTCF	chr3:119278367-119278703	H1-hESC	embryonic stem cell:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
23	POLR2A	chr3:119278220-119279228	GM12891	blood:	n/a	n/a
24	BHLHE40	chr3:119277581-119278720	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:119278223-119279588	GM12891	blood:	n/a	n/a
26	CTCF	chr3:119278331-119278753	A549	lung:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
27	TAF1	chr3:119278330-119278706	GM12892	blood:	n/a	n/a
28	POLR2A	chr3:119277583-119279649	GM12891	blood:	n/a	n/a
29	ZNF143	chr3:119277717-119278776	GM12878	blood:	n/a	n/a
30	CTCF	chr3:119278011-119279041	GM12878	blood:	n/a	chr3:119278958-119278967 chr3:119278181-119278202 chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
31	RAD21	chr3:119278293-119278779	MCF-7	breast:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
32	RAD21	chr3:119278217-119278723	A549	lung:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
33	CHD2	chr3:119278313-119278792	GM12878	blood:	n/a	n/a
34	YY1	chr3:119278320-119278764	GM12878	blood:	n/a	n/a
35	PML	chr3:119277538-119279835	GM12878	blood:	n/a	n/a
36	STAT3	chr3:119277801-119278809	GM12878	blood:	n/a	n/a
37	RELA	chr3:119277799-119279383	GM19099	blood:	n/a	n/a
38	NFIC	chr3:119277993-119278781	GM12878	blood:	n/a	n/a
39	CTCF	chr3:119278660-119278810	K562	blood:	n/a	n/a
40	CTCF	chr3:119278640-119278790	NHDF-neo	bronchial:	n/a	n/a
41	STAT5A	chr3:119277527-119279616	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:119278285-119279529	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:119278157-119279235	GM18951	blood:	n/a	n/a
44	POLR2A	chr3:119277989-119279676	GM12892	blood:	n/a	n/a
45	BCLAF1	chr3:119278013-119279568	GM12878	blood:	n/a	n/a
46	CTCF	chr3:119278405-119278734	Fibrobl	skin:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
47	FOXM1	chr3:119277650-119279476	GM12878	blood:	n/a	n/a
48	CTCF	chr3:119278660-119278810	AG04450	lung:	n/a	n/a
49	POLR2A	chr3:119278222-119278787	GM12891	blood:	n/a	n/a
50	POLR2A	chr3:119278341-119279509	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119181171..119183307-chr3:119278520..119281290,2	MCF-7	breast:
2	chr3:119218133..119220642-chr3:119277892..119280066,2	K562	blood:

Variant related genes	Relation type
CD80	TF binding region
ENSG00000176142	Chromatin interaction
ENSG00000113845	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10511393	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934494	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11533815	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11543525	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12487080	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487334	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487335	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487430	0.95[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	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494369	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494451	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12495673	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496129	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496520	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496841	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16829980	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829988	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16830002	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830004	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830008	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1852212	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2222630	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2222791	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34394661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915165	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915166	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271391	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4330287	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4407429	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55668872	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs55697229	0.81[AMR][1000 genomes]
rs55702208	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55738731	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55758148	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55772114	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55845727	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55848839	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55916342	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025972	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56078908	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56086928	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56124423	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56135341	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56213221	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58613639	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58924738	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59223102	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59374417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59529797	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59639276	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59654143	0.81[AMR][1000 genomes]
rs59701395	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59762006	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59764999	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59828023	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60920700	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61692996	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61702127	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438537	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66604554	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66797637	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66918189	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66920439	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67108211	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67160040	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67185025	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67212262	0.95[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	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67651191	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67765368	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68180496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72953001	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73189896	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73189897	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73189899	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs762629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885654	0.89[AMR][1000 genomes];1.00[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
rs41271393	CD80	cis	Muscle Skeletal	GTEx

Chromatin state (count:38 , 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	chr3:119275000-119281200	Weak transcription	Right Atrium	heart
4	chr3:119275000-119281200	Weak transcription	Spleen	Spleen
5	chr3:119276600-119279200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:119277000-119281200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:119277600-119278800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:119277600-119278800	Enhancers	Primary B cells from cord blood	blood
9	chr3:119277800-119279200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:119278000-119278800	Enhancers	Primary hematopoietic stem cells	blood
11	chr3:119278000-119278800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:119278000-119278800	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr3:119278200-119278800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:119278200-119278800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr3:119278200-119279000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr3:119278200-119279000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr3:119278200-119279000	Active TSS	Hela-S3	cervix
18	chr3:119278400-119278800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr3:119278400-119278800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:119278400-119278800	Active TSS	A549	lung
21	chr3:119278400-119279000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr3:119278400-119279000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:119278400-119279000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:119278400-119279000	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:119278400-119279400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:119278400-119282200	Enhancers	Primary B cells from peripheral blood	blood
27	chr3:119278600-119278800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:119278600-119278800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:119278600-119278800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:119278600-119278800	Enhancers	Pancreas	Pancrea
31	chr3:119278600-119278800	Enhancers	Dnd41	blood
32	chr3:119278600-119278800	Flanking Active TSS	HepG2	liver
33	chr3:119278600-119278800	Enhancers	K562	blood
34	chr3:119278600-119279000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr3:119278600-119279000	Enhancers	Fetal Thymus	thymus
36	chr3:119278600-119279000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr3:119278600-119279200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:119278600-119279600	Flanking Active TSS	GM12878-XiMat	blood

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