Variant report

Variant	rs523886
Chromosome Location	chr3:159734858-159734859
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	RFX5	chr3:159734785-159735099	Hela-S3	cervix:	n/a	n/a
2	ESR1	chr3:159734730-159735167	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr3:159734716-159735053	Hela-S3	cervix:	n/a	n/a
4	ZKSCAN1	chr3:159734777-159735007	Hela-S3	cervix:	n/a	n/a
5	FOS	chr3:159734731-159735088	MCF10A-Er-Src	breast:	n/a	chr3:159734914-159734923 chr3:159734915-159734924
6	NR2F2	chr3:159734554-159735322	MCF-7	breast:	n/a	n/a
7	TCF7L2	chr3:159734748-159735093	Hela-S3	cervix:	n/a	chr3:159734914-159734923
8	CHD2	chr3:159734813-159735060	Hela-S3	cervix:	n/a	n/a
9	FOS	chr3:159734770-159735073	MCF10A-Er-Src	breast:	n/a	chr3:159734914-159734923 chr3:159734915-159734924
10	NFIC	chr3:159734651-159735119	SK-N-SH	brain:	n/a	n/a
11	FOSL2	chr3:159734609-159735161	MCF-7	breast:	n/a	chr3:159734914-159734923 chr3:159734623-159734634 chr3:159734912-159734923 chr3:159734915-159734924
12	HDAC2	chr3:159734697-159735151	MCF-7	breast:	n/a	chr3:159734939-159734947
13	MAFK	chr3:159734837-159735038	HepG2	liver:	n/a	n/a
14	PBX3	chr3:159734767-159735062	SK-N-SH	brain:	n/a	n/a
15	TCF7L2	chr3:159734725-159735119	MCF-7	breast:	n/a	chr3:159734914-159734923
16	SMC3	chr3:159734786-159735073	Hela-S3	cervix:	n/a	n/a
17	RAD21	chr3:159734826-159735054	Hela-S3	cervix:	n/a	n/a
18	ARID3A	chr3:159734744-159735049	HepG2	liver:	n/a	n/a
19	JUN	chr3:159734740-159735026	HepG2	liver:	n/a	chr3:159734914-159734923 chr3:159734915-159734924
20	FOSL2	chr3:159734705-159735003	A549	lung:	n/a	chr3:159734914-159734923 chr3:159734912-159734923 chr3:159734915-159734924
21	GATA3	chr3:159734672-159735141	MCF-7	breast:	n/a	n/a
22	FOSL2	chr3:159734690-159735098	HepG2	liver:	n/a	chr3:159734914-159734923 chr3:159734912-159734923 chr3:159734915-159734924
23	FOSL2	chr3:159734653-159735106	A549	lung:	n/a	chr3:159734914-159734923 chr3:159734912-159734923 chr3:159734915-159734924
24	GATA3	chr3:159734745-159735167	MCF-7	breast:	n/a	n/a
25	NR2F2	chr3:159734514-159735276	MCF-7	breast:	n/a	n/a
26	STAT3	chr3:159734800-159735105	Hela-S3	cervix:	n/a	n/a
27	ESR1	chr3:159734746-159735077	ECC-1	luminal epithelium:	n/a	n/a
28	RCOR1	chr3:159734842-159735053	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr3:159734746-159735090	Hela-S3	cervix:	n/a	n/a
30	NFIC	chr3:159734668-159735118	ECC-1	luminal epithelium:	n/a	n/a
31	ZNF143	chr3:159734804-159734995	Hela-S3	cervix:	n/a	n/a
32	ZNF217	chr3:159734764-159735114	MCF-7	breast:	n/a	n/a
33	MYC	chr3:159734791-159735068	MCF10A-Er-Src	breast:	n/a	n/a
34	JUND	chr3:159734730-159735106	Hela-S3	cervix:	n/a	chr3:159734914-159734923 chr3:159734913-159734924 chr3:159734915-159734924
35	EP300	chr3:159734746-159735105	Hela-S3	cervix:	n/a	n/a
36	FOS	chr3:159734728-159735107	MCF10A-Er-Src	breast:	n/a	chr3:159734914-159734923 chr3:159734915-159734924
37	JUND	chr3:159734785-159735063	K562	blood:	n/a	chr3:159734914-159734923 chr3:159734913-159734924 chr3:159734915-159734924
38	FOS	chr3:159734701-159735099	Hela-S3	cervix:	n/a	chr3:159734914-159734923 chr3:159734915-159734924
39	JUN	chr3:159734739-159735116	Hela-S3	cervix:	n/a	chr3:159734914-159734923 chr3:159734915-159734924
40	ESR1	chr3:159734783-159735154	ECC-1	luminal epithelium:	n/a	n/a
41	FOXA2	chr3:159734778-159735088	HepG2	liver:	n/a	n/a
42	PBX3	chr3:159734815-159734999	GM12878	blood:	n/a	n/a
43	STAT3	chr3:159734734-159735078	MCF10A-Er-Src	breast:	n/a	n/a
44	FOS	chr3:159734728-159735088	MCF10A-Er-Src	breast:	n/a	chr3:159734914-159734923 chr3:159734915-159734924
45	HDAC2	chr3:159734617-159735114	MCF-7	breast:	n/a	chr3:159734939-159734947
46	EP300	chr3:159734601-159735087	MCF-7	breast:	n/a	n/a
47	GTF2F1	chr3:159734721-159735062	Hela-S3	cervix:	n/a	n/a
48	FOSL2	chr3:159734685-159735153	MCF-7	breast:	n/a	chr3:159734914-159734923 chr3:159734912-159734923 chr3:159734915-159734924
49	MAFK	chr3:159734782-159735044	Hela-S3	cervix:	n/a	n/a
50	MYC	chr3:159734807-159735000	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
IL12A-AS1	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11708713	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716424	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716451	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1651081	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874886	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2366643	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366644	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2647928	0.89[EUR][1000 genomes]
rs2647930	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914116	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936302	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936303	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580600	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4679867	0.94[EUR][1000 genomes]
rs4680536	0.87[EUR][1000 genomes]
rs4680538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680539	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs480134	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480913	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484600	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485499	0.93[EUR][1000 genomes]
rs485789	0.96[EUR][1000 genomes]
rs491966	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526734	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs545143	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545232	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547875	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548018	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564799	0.97[EUR][1000 genomes]
rs564976	0.97[EUR][1000 genomes]
rs571099	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574808	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579079	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586094	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs587422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs588998	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs589446	0.96[EUR][1000 genomes]
rs589545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62270441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629209	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441289	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441290	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669003	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771363	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808498	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808518	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640862	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9290051	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9845010	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829769	chr3:159606913-159805282	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv1806743	chr3:159723529-159744022	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159729200-159740800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:159730800-159739000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:159730800-159739000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:159731000-159736800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:159733800-159735000	Enhancers	NHLF	lung
6	chr3:159734400-159735000	Enhancers	Hela-S3	cervix
7	chr3:159734400-159735000	Enhancers	NHDF-Ad	bronchial
8	chr3:159734600-159735000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:159734600-159735000	Enhancers	Duodenum Mucosa	Duodenum
10	chr3:159734600-159735000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr3:159734600-159735000	Enhancers	A549	lung
12	chr3:159734600-159735000	Enhancers	HSMMtube	muscle
13	chr3:159734600-159735200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr3:159734800-159735000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:159734800-159735200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:159734800-159735200	Enhancers	HSMM	muscle
17	chr3:159734800-159735600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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