Variant report

Variant	rs539606499
Chromosome Location	chr3:134069566-134069567
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	NFIC	chr3:134069556-134070320	ECC-1	luminal epithelium:	n/a	chr3:134070094-134070111
2	POLR2A	chr3:134069330-134070156	ECC-1	luminal epithelium:	n/a	n/a
3	SP1	chr3:134069500-134070311	HCT-116	colon:	n/a	chr3:134069739-134069753 chr3:134070106-134070120
4	TCF12	chr3:134069386-134070624	MCF-7	breast:	n/a	chr3:134069806-134069813 chr3:134069732-134069742 chr3:134070314-134070324
5	MAX	chr3:134069551-134070304	HCT-116	colon:	n/a	chr3:134069852-134069861
6	ELF1	chr3:134069177-134070324	MCF-7	breast:	n/a	n/a
7	POLR2A	chr3:134069439-134070162	MCF-7	breast:	n/a	n/a
8	MAX	chr3:134069542-134070379	HCT-116	colon:	n/a	chr3:134069852-134069861
9	TCF12	chr3:134069540-134070380	ECC-1	luminal epithelium:	n/a	chr3:134069806-134069813 chr3:134069732-134069742 chr3:134070314-134070324
10	MAX	chr3:134069228-134070274	MCF-7	breast:	n/a	chr3:134069852-134069861
11	TCF12	chr3:134069464-134070399	ECC-1	luminal epithelium:	n/a	chr3:134069806-134069813 chr3:134069732-134069742 chr3:134070314-134070324
12	JUND	chr3:134069558-134070232	HCT-116	colon:	n/a	n/a
13	GATA3	chr3:134069560-134070443	MCF-7	breast:	n/a	chr3:134069698-134069707
14	POLR2A	chr3:134069255-134074808	A549	lung:	n/a	n/a
15	TCF12	chr3:134069559-134070425	MCF-7	breast:	n/a	chr3:134069806-134069813 chr3:134069732-134069742 chr3:134070314-134070324
16	GATA3	chr3:134069445-134070537	MCF-7	breast:	n/a	chr3:134069698-134069707
17	POLR2A	chr3:134069087-134070157	ECC-1	luminal epithelium:	n/a	n/a
18	SIN3AK20	chr3:134069391-134070562	MCF-7	breast:	n/a	n/a
19	POLR2A	chr3:134069355-134094620	IMR90	lung:	n/a	n/a
20	EP300	chr3:134069506-134070423	ECC-1	luminal epithelium:	n/a	chr3:134070194-134070204 chr3:134070406-134070420
21	FOSL1	chr3:134069546-134070236	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:134068339..134071562-chr3:134203031..134205941,6	MCF-7	breast:
2	chr3:134019644..134021494-chr3:134068815..134070339,2	MCF-7	breast:
3	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
4	chr3:134066447..134072766-chr3:134202428..134206376,9	MCF-7	breast:
5	chr3:134031725..134032254-chr3:134069181..134070038,2	MCF-7	breast:
6	chr3:133967562..133971327-chr3:134067822..134072418,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260633	TF binding region
ENSG00000240006	Chromatin interaction
ENSG00000163785	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv967066	chr3:134069560-134071258	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134054200-134069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:134055800-134071000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:134060600-134070000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:134060800-134072200	Weak transcription	Fetal Kidney	kidney
5	chr3:134061400-134073000	Weak transcription	Fetal Brain Male	brain
6	chr3:134065800-134071400	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:134065800-134071400	Enhancers	Fetal Intestine Large	intestine
8	chr3:134065800-134071600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:134065800-134072400	Weak transcription	Spleen	Spleen
10	chr3:134066000-134072800	Enhancers	Duodenum Mucosa	Duodenum
11	chr3:134066200-134069600	Weak transcription	A549	lung
12	chr3:134066200-134071000	Weak transcription	Brain Substantia Nigra	brain
13	chr3:134066400-134071400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr3:134066400-134071600	Weak transcription	Fetal Lung	lung
15	chr3:134066400-134071600	Enhancers	Placenta	Placenta
16	chr3:134066400-134073000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr3:134066600-134069800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:134066600-134071800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr3:134066600-134076200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:134066800-134069600	Weak transcription	HepG2	liver
21	chr3:134066800-134073000	Weak transcription	Ovary	ovary
22	chr3:134067000-134073400	Enhancers	Pancreas	Pancrea
23	chr3:134067200-134071600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:134067200-134071800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:134067200-134072000	Enhancers	HMEC	breast
26	chr3:134067200-134072800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:134067200-134073000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:134067400-134073200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:134067400-134073200	Enhancers	Esophagus	oesophagus
30	chr3:134067600-134072800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:134067600-134073200	Weak transcription	Brain Angular Gyrus	brain
32	chr3:134067600-134076200	Strong transcription	Brain Germinal Matrix	brain
33	chr3:134067800-134069800	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:134067800-134072400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:134067800-134073000	Weak transcription	Brain Anterior Caudate	brain
36	chr3:134067800-134073200	Weak transcription	NH-A	brain
37	chr3:134068000-134069800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:134068200-134069800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:134068200-134069800	Weak transcription	Aorta	Aorta
40	chr3:134068200-134069800	Weak transcription	Hela-S3	cervix
41	chr3:134068200-134070200	Weak transcription	Osteobl	bone
42	chr3:134068200-134071000	Weak transcription	NHLF	lung
43	chr3:134068400-134070200	Weak transcription	NHDF-Ad	bronchial
44	chr3:134068400-134070400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:134068400-134071200	Weak transcription	Fetal Heart	heart
46	chr3:134068400-134072800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:134068400-134073200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:134068400-134074200	Genic enhancers	Fetal Intestine Small	intestine
49	chr3:134068400-134076000	Strong transcription	Fetal Stomach	stomach
50	chr3:134068800-134071800	Enhancers	NHEK	skin

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