Variant report

Variant	rs528646517
Chromosome Location	chr2:39892534-39892535
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:39892356-39892556	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF143	chr2:39892288-39893212	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr2:39892143-39892589	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3A	chr2:39892127-39894357	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr2:39892304-39892601	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr2:39892043-39892640	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD1	chr2:39892496-39892674	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3AK20	chr2:39892465-39892795	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr2:39891897-39892587	H1-hESC	embryonic stem cell:	n/a	n/a
10	TBP	chr2:39892238-39892559	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr2:39892088-39892803	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTBP2	chr2:39892004-39892716	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr2:39892498-39892649	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:39892502-39892552	GM12878	blood:	n/a
2	chr2:39892502-39892552	GM06990	blood:	n/a
3	chr2:39892502-39892552	SK-N-SH_RA	brain:	n/a
4	chr2:39892502-39892552	AG09309	skin:	n/a
5	chr2:39892502-39892552	IMR90	lung:	fetal
6	chr2:39892502-39892552	HCM	heart:	n/a
7	chr2:39892502-39892552	NH-A	brain:	n/a
8	chr2:39892502-39892552	Hepatocyte	liver:	n/a
9	chr2:39892502-39892552	NB4	blood:	n/a
10	chr2:39892502-39892552	U87	brain:	n/a
11	chr2:39892502-39892552	SAEC	small airway:	n/a
12	chr2:39892502-39892552	HUVEC	blood vessel:	n/a
13	chr2:39892502-39892552	SK-N-MC	brain:	n/a
14	chr2:39892502-39892552	NHBE	bronchial:	n/a
15	chr2:39892502-39892552	HMEC	breast:	n/a
16	chr2:39892502-39892552	HRCEpiC	kidney:	n/a
17	chr2:39892502-39892552	SK-N-SH	brain:	n/a
18	chr2:39892502-39892552	HCF	heart:	n/a
19	chr2:39892502-39892552	T-47D	breast:	n/a
20	chr2:39892502-39892552	ovcar-3	ovarian:	n/a
21	chr2:39892502-39892552	PrEC	prostate:	n/a
22	chr2:39892502-39892552	SKMC	muscle:	n/a
23	chr2:39892502-39892552	GM19239	blood:	n/a
24	chr2:39892502-39892552	HCPEpiC	choroid plexus:	n/a
25	chr2:39892502-39892552	BJ	skin:	n/a
26	chr2:39892502-39892552	BE2_C	brain:	n/a
27	chr2:39892502-39892552	Jurkat	blood:	n/a
28	chr2:39892502-39892552	RPTEC	kidney:	n/a
29	chr2:39892502-39892552	NHDF-neo	bronchial:	n/a
30	chr2:39892502-39892552	HEEpiC	esophagus:	n/a
31	chr2:39892502-39892552	PFSK-1	brain:	n/a
32	chr2:39892502-39892552	MCF10A-Er-Src	breast:	n/a
33	chr2:39892502-39892552	PANC-1	pancreas:	n/a
34	chr2:39892502-39892552	AG09319	gingival:	n/a
35	chr2:39892502-39892552	HRE	kidney:	n/a
36	chr2:39892502-39892552	HL-60	blood:	n/a
37	chr2:39892502-39892552	HAEpiC	amniotic membrane:	n/a
38	chr2:39892502-39892552	HCT-116	colon:	n/a
39	chr2:39892502-39892552	HPAEpiC	pulmonary alveolar:	n/a
40	chr2:39892502-39892552	AG04450	lung:	fetal
41	chr2:39892502-39892552	CMK	blood:	n/a
42	chr2:39892502-39892552	HEK293	kidney:	embryo
43	chr2:39892502-39892552	GM12892	blood:	n/a
44	chr2:39892502-39892552	H1-hESC	embryonic stem cell:	embryo
45	chr2:39892502-39892552	Caco-2	colon:	n/a
46	chr2:39892502-39892552	LNCaP	prostate:	n/a
47	chr2:39892502-39892552	NT2-D1	testis:	n/a
48	chr2:39892502-39892552	Hela-S3	cervix:	n/a
49	chr2:39892502-39892552	HIPEpiC	eye:	n/a
50	chr2:39892502-39892552	K562	blood:	n/a

No data

Variant related genes	Relation type
TMEM178A	TF binding region
TMEM178A	CpG island

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3411574	chr2:39891873-39894421	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3377107	chr2:39892273-39894821	Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39885600-39893600	Weak transcription	Fetal Brain Male	brain
2	chr2:39890000-39892600	Weak transcription	HSMMtube	muscle
3	chr2:39891200-39894000	Active TSS	Fetal Brain Female	brain
4	chr2:39891600-39892600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
5	chr2:39891800-39892800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
6	chr2:39891800-39893000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:39891800-39894600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr2:39892000-39893800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:39892000-39893800	Active TSS	HSMM	muscle
10	chr2:39892000-39894000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr2:39892000-39894200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr2:39892000-39894400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:39892200-39892600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:39892200-39892600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:39892200-39892600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr2:39892200-39892600	Flanking Bivalent TSS/Enh	HepG2	liver
17	chr2:39892200-39892800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:39892200-39892800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
19	chr2:39892200-39893200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:39892200-39893600	Active TSS	Brain Anterior Caudate	brain
21	chr2:39892200-39893600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr2:39892200-39893600	Active TSS	Fetal Muscle Trunk	muscle
23	chr2:39892200-39893800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:39892200-39893800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:39892200-39893800	Bivalent/Poised TSS	Fetal Lung	lung
26	chr2:39892200-39894000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
27	chr2:39892200-39894000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:39892200-39894000	Active TSS	H9 Cell Line	embryonic stem cell
29	chr2:39892200-39894000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:39892200-39894000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr2:39892200-39894000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:39892200-39894000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:39892200-39894000	Active TSS	Fetal Kidney	kidney
34	chr2:39892200-39894600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr2:39892400-39892600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr2:39892400-39892600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:39892400-39892600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:39892400-39892600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:39892400-39892600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:39892400-39892600	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr2:39892400-39892600	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr2:39892400-39892600	Bivalent Enhancer	Fetal Intestine Large	intestine
43	chr2:39892400-39892600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
44	chr2:39892400-39892600	Bivalent Enhancer	NHEK	skin
45	chr2:39892400-39892800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
46	chr2:39892400-39892800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:39892400-39892800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
48	chr2:39892400-39892800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
49	chr2:39892400-39892800	Active TSS	Fetal Heart	heart
50	chr2:39892400-39893200	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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