Variant report

Variant	rs16829309
Chromosome Location	chr3:158414757-158414758
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	E2F4	chr3:158414317-158414787	MCF10A-Er-Src	breast:	n/a	n/a
2	FOXA1	chr3:158414508-158414843	HepG2	liver:	n/a	n/a
3	SP1	chr3:158414386-158414867	A549	lung:	n/a	n/a
4	NR3C1	chr3:158414662-158414795	A549	lung:	n/a	n/a
5	EP300	chr3:158414310-158415048	A549	lung:	n/a	chr3:158414639-158414649
6	FOXA1	chr3:158414442-158414839	HepG2	liver:	n/a	n/a
7	JUND	chr3:158414429-158414828	T-47D	breast:	n/a	chr3:158414544-158414556
8	GATA3	chr3:158414400-158415037	A549	lung:	n/a	n/a
9	FOXA1	chr3:158414408-158414871	HepG2	liver:	n/a	n/a
10	TCF12	chr3:158414211-158415039	A549	lung:	n/a	n/a
11	CEBPB	chr3:158414408-158414994	A549	lung:	n/a	n/a
12	FOXA1	chr3:158414454-158414844	T-47D	breast:	n/a	n/a
13	CEBPB	chr3:158414432-158414801	HepG2	liver:	n/a	n/a
14	FOXA2	chr3:158414498-158414816	HepG2	liver:	n/a	n/a
15	REST	chr3:158414353-158414963	A549	lung:	n/a	n/a
16	FOSL2	chr3:158414365-158415005	A549	lung:	n/a	chr3:158414544-158414556
17	CEBPB	chr3:158414371-158414854	IMR90	lung:	n/a	n/a
18	EP300	chr3:158414287-158414964	A549	lung:	n/a	chr3:158414639-158414649
19	SP1	chr3:158414347-158415065	A549	lung:	n/a	n/a
20	GATA3	chr3:158414568-158414876	T-47D	breast:	n/a	n/a
21	GATA3	chr3:158414404-158414961	A549	lung:	n/a	n/a
22	FOXA2	chr3:158414388-158415091	A549	lung:	n/a	n/a
23	EP300	chr3:158414472-158414792	K562	blood:	n/a	chr3:158414639-158414649
24	FOXA1	chr3:158414363-158414954	A549	lung:	n/a	n/a
25	TCF7L2	chr3:158414462-158414860	PANC-1	pancreas:	n/a	n/a
26	BCL3	chr3:158414350-158414962	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000272087	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16829140	1.00[YRI][hapmap]
rs16829307	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35475848	1.00[EUR][1000 genomes]
rs60460783	1.00[EUR][1000 genomes]
rs9877427	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158390400-158416800	Weak transcription	Aorta	Aorta
2	chr3:158390400-158428600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:158390600-158427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:158390800-158416800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:158390800-158425400	Weak transcription	Fetal Brain Female	brain
6	chr3:158390800-158427000	Weak transcription	Brain Angular Gyrus	brain
7	chr3:158390800-158427400	Weak transcription	Esophagus	oesophagus
8	chr3:158390800-158427400	Weak transcription	Lung	lung
9	chr3:158390800-158429400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:158390800-158430200	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:158390800-158430400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:158390800-158430800	Weak transcription	Right Ventricle	heart
13	chr3:158390800-158430800	Weak transcription	Stomach Mucosa	stomach
14	chr3:158390800-158432800	Weak transcription	Spleen	Spleen
15	chr3:158390800-158444200	Weak transcription	Gastric	stomach
16	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:158391000-158418600	Weak transcription	Fetal Brain Male	brain
18	chr3:158391000-158421000	Weak transcription	Fetal Heart	heart
19	chr3:158391000-158427200	Weak transcription	NHEK	skin
20	chr3:158391000-158427400	Weak transcription	Pancreas	Pancrea
21	chr3:158391000-158429200	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:158391000-158430600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:158391000-158438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:158395800-158420800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:158395800-158423000	Weak transcription	Fetal Stomach	stomach
26	chr3:158396200-158418400	Weak transcription	Brain Germinal Matrix	brain
27	chr3:158397000-158429200	Weak transcription	Ovary	ovary
28	chr3:158397000-158443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
30	chr3:158397800-158425200	Weak transcription	HSMMtube	muscle
31	chr3:158399600-158445400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:158400600-158429000	Weak transcription	Brain Substantia Nigra	brain
33	chr3:158403600-158438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:158403800-158420800	Weak transcription	HMEC	breast
35	chr3:158408000-158417800	Strong transcription	Fetal Intestine Large	intestine
36	chr3:158408400-158430200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:158408400-158443000	Weak transcription	HepG2	liver
38	chr3:158408600-158419400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:158408800-158422400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:158409000-158429800	Weak transcription	Small Intestine	intestine
41	chr3:158409200-158421200	Weak transcription	Psoas Muscle	Psoas
42	chr3:158409200-158427400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:158409400-158415200	Weak transcription	NH-A	brain
44	chr3:158409400-158425400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:158409400-158425600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:158409400-158426200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:158409400-158426800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:158409400-158427200	Weak transcription	Brain Anterior Caudate	brain
49	chr3:158409600-158417600	Weak transcription	NHDF-Ad	bronchial
50	chr3:158409800-158439000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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