Variant report

Variant	rs139388579
Chromosome Location	chr3:52742362-52742363
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	chr3:52742145-52742715	K562	blood:	n/a	n/a
2	POLR2A	chr3:52742120-52742560	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52718628..52724105-chr3:52738117..52743946,12	MCF-7	breast:
2	chr3:52738473..52741784-chr3:52742214..52745484,3	MCF-7	breast:

Variant related genes	Relation type
GLT8D1	TF binding region
ENSG00000252787	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000212493	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000114902	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking 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 target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52739000-52742600	Active TSS	GM12878-XiMat	blood
2	chr3:52740600-52742400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr3:52741000-52742400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:52741000-52742400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr3:52741000-52746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:52741000-52748200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:52741000-52748200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:52741000-52748800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:52741000-52748800	Weak transcription	Lung	lung
10	chr3:52741200-52742400	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr3:52741200-52742400	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:52741200-52748200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:52741400-52742400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
14	chr3:52741400-52746600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:52741400-52747000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:52741400-52765600	Weak transcription	Aorta	Aorta
17	chr3:52741400-52766600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:52741600-52742400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr3:52741600-52742400	Genic enhancers	Primary B cells from peripheral blood	blood
20	chr3:52741600-52742400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr3:52741600-52742400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:52741600-52742400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
23	chr3:52741600-52742400	Enhancers	Pancreas	Pancrea
24	chr3:52741600-52742800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:52741600-52743000	Strong transcription	NHDF-Ad	bronchial
26	chr3:52741600-52743600	Weak transcription	Left Ventricle	heart
27	chr3:52741600-52746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:52741600-52746400	Weak transcription	Gastric	stomach
29	chr3:52741600-52746400	Weak transcription	Spleen	Spleen
30	chr3:52741600-52746600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:52741600-52747000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:52741600-52747000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:52741600-52748000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:52741600-52748200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:52741600-52748200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:52741600-52748400	Weak transcription	Colonic Mucosa	Colon
37	chr3:52741600-52748400	Weak transcription	Right Ventricle	heart
38	chr3:52741600-52748600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:52741600-52748600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:52741600-52752600	Weak transcription	Ovary	ovary
41	chr3:52741600-52752600	Weak transcription	A549	lung
42	chr3:52741600-52764000	Weak transcription	Small Intestine	intestine
43	chr3:52741600-52765600	Weak transcription	Esophagus	oesophagus
44	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
45	chr3:52741800-52742400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:52741800-52742400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr3:52741800-52742400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr3:52741800-52742400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:52741800-52742400	Genic enhancers	Fetal Thymus	thymus
50	chr3:52741800-52742400	Genic enhancers	Rectal Mucosa Donor 29	rectum

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