Variant report

Variant	rs28475027
Chromosome Location	chr3:20150483-20150484
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	GATA3	chr3:20150247-20151059	MCF-7	breast:	n/a	n/a
2	TCF7L2	chr3:20150402-20150937	MCF-7	breast:	n/a	chr3:20150625-20150639
3	GATA3	chr3:20150299-20150985	MCF-7	breast:	n/a	n/a
4	CEBPB	chr3:20150405-20150826	A549	lung:	n/a	n/a
5	CEBPB	chr3:20150386-20151028	MCF-7	breast:	n/a	n/a
6	GATA3	chr3:20150335-20150775	T-47D	breast:	n/a	n/a
7	STAT3	chr3:20150417-20150817	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr3:20150448-20150779	MCF10A-Er-Src	breast:	n/a	n/a
9	GATA3	chr3:20150066-20151130	MCF-7	breast:	n/a	n/a
10	STAT3	chr3:20150415-20151008	MCF10A-Er-Src	breast:	n/a	n/a
11	GATA3	chr3:20150370-20150769	T-47D	breast:	n/a	n/a
12	HDAC2	chr3:20150365-20150938	MCF-7	breast:	n/a	n/a
13	FOS	chr3:20150408-20150783	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr3:20150435-20150783	MCF10A-Er-Src	breast:	n/a	n/a
15	SIN3AK20	chr3:20150329-20151104	MCF-7	breast:	n/a	n/a
16	SIN3AK20	chr3:20150344-20150999	MCF-7	breast:	n/a	n/a
17	JUND	chr3:20150339-20150951	MCF-7	breast:	n/a	n/a
18	FOSL2	chr3:20150455-20150836	MCF-7	breast:	n/a	n/a
19	CEBPB	chr3:20150443-20150753	A549	lung:	n/a	n/a
20	TCF12	chr3:20150348-20150907	MCF-7	breast:	n/a	n/a
21	GATA3	chr3:20150466-20150933	MCF-7	breast:	n/a	n/a
22	HDAC2	chr3:20150313-20150942	MCF-7	breast:	n/a	n/a
23	FOXA1	chr3:20150399-20150645	T-47D	breast:	n/a	n/a
24	ZNF217	chr3:20150422-20150942	MCF-7	breast:	n/a	n/a
25	CEBPB	chr3:20150459-20150847	K562	blood:	n/a	n/a
26	FOS	chr3:20150430-20150805	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr3:20150445-20150639	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr3:20150431-20150780	MCF10A-Er-Src	breast:	n/a	n/a
29	CEBPB	chr3:20150404-20150987	MCF-7	breast:	n/a	n/a
30	FOXA2	chr3:20150321-20150636	A549	lung:	n/a	n/a
31	FOS	chr3:20150410-20150775	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
KAT2B	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS 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	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers 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 miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
14	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
16	esv3394910	chr3:20150394-20203576	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
17	esv3334928	chr3:20150414-20203546	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
2	chr3:20123000-20153000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:20123200-20153200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:20128200-20175800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:20131800-20153000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:20132800-20152400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:20135200-20173800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:20137400-20156600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:20137600-20153000	Weak transcription	Spleen	Spleen
10	chr3:20137800-20153000	Weak transcription	Esophagus	oesophagus
11	chr3:20137800-20153000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:20137800-20153200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:20138000-20152800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:20138000-20153000	Weak transcription	Aorta	Aorta
15	chr3:20138000-20153000	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:20138800-20152600	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:20138800-20156400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:20139000-20152800	Weak transcription	Liver	Liver
19	chr3:20139000-20152800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:20139000-20164000	Weak transcription	Small Intestine	intestine
21	chr3:20139800-20161000	Weak transcription	Fetal Intestine Small	intestine
22	chr3:20141000-20153200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:20141200-20153000	Weak transcription	Fetal Lung	lung
24	chr3:20141200-20167400	Weak transcription	HSMMtube	muscle
25	chr3:20141200-20222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:20141800-20153000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:20141800-20153000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:20142200-20152600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:20142600-20189400	Weak transcription	Fetal Brain Male	brain
30	chr3:20143200-20150800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:20143200-20152800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:20143200-20152800	Weak transcription	Left Ventricle	heart
33	chr3:20143200-20153000	Weak transcription	Adipose Nuclei	Adipose
34	chr3:20143200-20153000	Weak transcription	Ovary	ovary
35	chr3:20143800-20152800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr3:20144600-20162000	Weak transcription	Fetal Heart	heart
37	chr3:20145400-20150800	Weak transcription	Fetal Thymus	thymus
38	chr3:20145800-20151800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:20146000-20156400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:20146000-20156400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:20146200-20152800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:20146200-20153200	Weak transcription	Brain Anterior Caudate	brain
43	chr3:20146200-20154200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:20146200-20156400	Weak transcription	Brain Angular Gyrus	brain
45	chr3:20146400-20152800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:20146400-20153000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:20146400-20157600	Weak transcription	Fetal Brain Female	brain
48	chr3:20146400-20163400	Weak transcription	Brain Germinal Matrix	brain
49	chr3:20147400-20169600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:20147600-20151600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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