Variant report

Variant	rs16829980
Chromosome Location	chr3:119278468-119278469
allele	A/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	POLR2A	chr3:119278283-119279546	Raji	blood:	n/a	n/a
2	ZNF143	chr3:119278334-119278691	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr3:119278366-119278618	K562	blood:	n/a	n/a
4	POLR2A	chr3:119278320-119279538	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:119278316-119278476	K562	blood:	n/a	n/a
6	CTCF	chr3:119278420-119278570	AG04450	lung:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
7	RAD21	chr3:119278396-119278581	K562	blood:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
8	CTCF	chr3:119278460-119278610	AG04449	skin:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
9	CTCF	chr3:119278420-119278570	HMF	breast:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
10	RCOR1	chr3:119278323-119278480	K562	blood:	n/a	n/a
11	CTCF	chr3:119278460-119278610	HA-sp	spinal cord:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
12	EBF1	chr3:119277828-119278760	GM12878	blood:	n/a	n/a
13	RAD21	chr3:119278282-119278698	H1-hESC	embryonic stem cell:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
14	CTCF	chr3:119278440-119278590	AG09319	gingival:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
15	ZMIZ1	chr3:119278447-119278703	K562	blood:	n/a	n/a
16	UBTF	chr3:119278288-119278656	K562	blood:	n/a	n/a
17	RAD21	chr3:119278217-119278791	H1-hESC	embryonic stem cell:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
18	CTCF	chr3:119278400-119278550	BJ	skin:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
19	CTCF	chr3:119278400-119278550	Hela-S3	cervix:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
20	RAD21	chr3:119278303-119278785	MCF-7	breast:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
21	RAD21	chr3:119278359-119278577	K562	blood:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
22	CTCF	chr3:119278391-119278660	K562	blood:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
23	RFX5	chr3:119278299-119278488	K562	blood:	n/a	n/a
24	RAD21	chr3:119278280-119278647	HepG2	liver:	n/a	chr3:119278510-119278529 chr3:119278514-119278528
25	CTCF	chr3:119278389-119278721	GM19240	blood:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
26	EP300	chr3:119278335-119278696	GM12878	blood:	n/a	chr3:119278387-119278401
27	CTCF	chr3:119278376-119278671	HepG2	liver:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
28	STAT5A	chr3:119278005-119278805	GM12878	blood:	n/a	n/a
29	CTCF	chr3:119278420-119278570	Caco-2	colon:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
30	CTCF	chr3:119278416-119278649	GM10266	blood:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
31	ZC3H11A	chr3:119278440-119278563	K562	blood:	n/a	n/a
32	ATF2	chr3:119277519-119278834	GM12878	blood:	n/a	n/a
33	CTCF	chr3:119278340-119278547	SK-N-SH_RA	brain:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
34	CTCF	chr3:119278440-119278590	GM12872	blood:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
35	CTCF	chr3:119278380-119278530	GM12868	blood:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
36	CTCF	chr3:119278400-119278550	AG04450	lung:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
37	POU2F2	chr3:119278263-119278900	GM12878	blood:	n/a	chr3:119278515-119278527 chr3:119278584-119278596
38	SMC3	chr3:119278332-119278698	K562	blood:	n/a	chr3:119278514-119278528
39	MAFK	chr3:119278280-119278502	K562	blood:	n/a	n/a
40	CTCF	chr3:119278440-119278590	GM12868	blood:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
41	PML	chr3:119278245-119278731	GM12878	blood:	n/a	n/a
42	CTCF	chr3:119278402-119278639	LNCaP	prostate:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
43	CTCF	chr3:119278440-119278590	HMEC	breast:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
44	CTCF	chr3:119278340-119278490	NHDF-neo	bronchial:	n/a	n/a
45	CTCF	chr3:119278360-119278510	HA-sp	spinal cord:	n/a	n/a
46	EP300	chr3:119278342-119278608	K562	blood:	n/a	chr3:119278387-119278401
47	CTCF	chr3:119278400-119278550	HMEC	breast:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
48	POLR2A	chr3:119278185-119279438	GM15510	blood:	n/a	n/a
49	CTCF	chr3:119278460-119278610	SK-N-SH_RA	brain:	n/a	chr3:119278514-119278527 chr3:119278512-119278530 chr3:119278513-119278529
50	TBL1XR1	chr3:119278218-119278720	GM12878	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934494	0.86[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	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487334	0.89[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	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487965	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489080	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492723	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494369	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494451	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12495673	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496129	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496520	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496841	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16829988	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16830002	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830004	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830008	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1852212	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019144	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2222630	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2222791	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34394661	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915165	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915166	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271391	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271393	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4330287	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4407429	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55668872	0.90[EUR][1000 genomes]
rs55702208	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55738731	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55758148	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55772114	0.95[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	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55916342	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025972	0.87[EUR][1000 genomes]
rs56078908	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56086928	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56124423	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56135341	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56213221	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58613639	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58924738	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59223102	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59374417	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59529797	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59639276	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59701395	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59762006	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59764999	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59828023	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60920700	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61692996	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61702127	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438537	0.98[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	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66918189	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66920439	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67108211	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67160040	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67185025	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67212262	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67307954	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67369952	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67651191	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67765368	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68180496	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72953001	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73189896	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73189897	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73189899	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs762629	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762631	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867234	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885654	0.84[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
rs16829980	CD80	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 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	chr3:119277000-119281200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:119277600-119278800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:119277600-119278800	Enhancers	Primary B cells from cord blood	blood
12	chr3:119277800-119279200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr3:119278000-119278800	Enhancers	Primary hematopoietic stem cells	blood
14	chr3:119278000-119278800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:119278000-119278800	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr3:119278200-119278600	Flanking Active TSS	K562	blood
17	chr3:119278200-119278800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:119278200-119278800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr3:119278200-119279000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr3:119278200-119279000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr3:119278200-119279000	Active TSS	Hela-S3	cervix
22	chr3:119278400-119278600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:119278400-119278600	Flanking Active TSS	Thymus	Thymus
24	chr3:119278400-119278800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr3:119278400-119278800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:119278400-119278800	Active TSS	A549	lung
27	chr3:119278400-119279000	Enhancers	Primary T cells fromperipheralblood	blood
28	chr3:119278400-119279000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:119278400-119279000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:119278400-119279000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr3:119278400-119279400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:119278400-119282200	Enhancers	Primary B cells from peripheral blood	blood

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