Variant report

Variant	rs564838908
Chromosome Location	chr3:52741991-52741992
allele	A/T
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	MEF2C	chr3:52741483-52742069	GM12878	blood:	n/a	chr3:52741652-52741673 chr3:52741811-52741826
2	NFIC	chr3:52741269-52742113	GM12878	blood:	n/a	n/a
3	ATF2	chr3:52741443-52742145	GM12878	blood:	n/a	n/a
4	SP1	chr3:52741606-52741993	H1-hESC	embryonic stem cell:	n/a	n/a
5	FOXM1	chr3:52741492-52742131	GM12878	blood:	n/a	n/a
6	STAT5A	chr3:52741401-52742079	GM12878	blood:	n/a	n/a
7	TCF3	chr3:52741717-52742110	GM12878	blood:	n/a	n/a
8	STAT5A	chr3:52741621-52742085	GM12878	blood:	n/a	n/a
9	MTA3	chr3:52741524-52742141	GM12878	blood:	n/a	n/a
10	PML	chr3:52741223-52742041	GM12878	blood:	n/a	n/a
11	CUX1	chr3:52741820-52742018	GM12878	blood:	n/a	n/a
12	RUNX3	chr3:52741360-52742165	GM12878	blood:	n/a	n/a
13	MEF2A	chr3:52741410-52742103	GM12878	blood:	n/a	chr3:52741652-52741673
14	NFIC	chr3:52741381-52742120	GM12878	blood:	n/a	n/a
15	SPI1	chr3:52741492-52742095	GM12878	blood:	n/a	chr3:52741681-52741694
16	MAZ	chr3:52741420-52741991	GM12878	blood:	n/a	n/a
17	RCOR1	chr3:52741541-52742019	GM12878	blood:	n/a	n/a
18	MEF2A	chr3:52741580-52742102	GM12878	blood:	n/a	chr3:52741652-52741673
19	BCLAF1	chr3:52741495-52742117	GM12878	blood:	n/a	n/a
20	BHLHE40	chr3:52741636-52742038	GM12878	blood:	n/a	n/a
21	MTA3	chr3:52741227-52742130	GM12878	blood:	n/a	n/a
22	RUNX3	chr3:52741295-52742097	GM12878	blood:	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	chr3:52569513..52572297-chr3:52740518..52742042,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GNL3-1	chr3:52741703-52742035	NONHSAT089952

Variant related genes	Relation type
GLT8D1	TF binding region
ENSG00000168273	Chromatin interaction
ENSG00000212493	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000252787	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:126 , 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	chr3:52740200-52742200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:52740400-52742000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr3:52740600-52742400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr3:52741000-52742000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:52741000-52742000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr3:52741000-52742000	Enhancers	Primary B cells from cord blood	blood
8	chr3:52741000-52742000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:52741000-52742200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:52741000-52742400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:52741000-52742400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:52741000-52746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:52741000-52748200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:52741000-52748200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:52741000-52748800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:52741000-52748800	Weak transcription	Lung	lung
17	chr3:52741200-52742000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:52741200-52742000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:52741200-52742000	Weak transcription	Fetal Kidney	kidney
20	chr3:52741200-52742200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:52741200-52742200	Enhancers	Colon Smooth Muscle	Colon
22	chr3:52741200-52742200	Enhancers	Fetal Brain Male	brain
23	chr3:52741200-52742400	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr3:52741200-52742400	Enhancers	Primary hematopoietic stem cells	blood
25	chr3:52741200-52748200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:52741400-52742000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:52741400-52742000	Genic enhancers	Liver	Liver
28	chr3:52741400-52742000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:52741400-52742000	Genic enhancers	Fetal Intestine Small	intestine
30	chr3:52741400-52742000	Flanking Active TSS	Hela-S3	cervix
31	chr3:52741400-52742000	Transcr. at gene 5' and 3'	HSMMtube	muscle
32	chr3:52741400-52742000	Flanking Active TSS	NHEK	skin
33	chr3:52741400-52742200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:52741400-52742400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
35	chr3:52741400-52746600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:52741400-52747000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:52741400-52765600	Weak transcription	Aorta	Aorta
38	chr3:52741400-52766600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:52741600-52742000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:52741600-52742000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:52741600-52742000	Genic enhancers	Fetal Lung	lung
42	chr3:52741600-52742000	Genic enhancers	Fetal Stomach	stomach
43	chr3:52741600-52742000	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr3:52741600-52742000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr3:52741600-52742000	Transcr. at gene 5' and 3'	NH-A	brain
46	chr3:52741600-52742000	Enhancers	NHLF	lung
47	chr3:52741600-52742200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:52741600-52742200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:52741600-52742200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr3:52741600-52742200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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