Variant report

Variant	rs56190300
Chromosome Location	chr1:153914500-153914501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153914316-153914638	A549	lung:	n/a	n/a
2	POLR2A	chr1:153914189-153914835	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:153914269-153914801	HL-60	blood:	n/a	n/a
4	POLR2A	chr1:153914399-153914673	A549	lung:	n/a	n/a
5	POLR2A	chr1:153914321-153914868	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:153913011-153915862	K562	blood:	n/a	n/a
7	POLR2A	chr1:153914431-153914726	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:153912647-153915284	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:153914347-153914746	A549	lung:	n/a	n/a
10	POLR2A	chr1:153913791-153915938	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr1:153914356-153914632	A549	lung:	n/a	n/a
12	POLR2A	chr1:153914244-153914532	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:153912970-153915800	K562	blood:	n/a	n/a
14	POLR2A	chr1:153914086-153915919	K562	blood:	n/a	n/a
15	POLR2A	chr1:153914252-153914686	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:153914349-153914760	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:153914265-153914773	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:153914473-153915120	GM12878	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:153914492-153914542	HMEC	breast:	n/a
2	chr1:153914492-153914542	Caco-2	colon:	n/a
3	chr1:153914492-153914542	AG09309	skin:	n/a
4	chr1:153914492-153914542	ProgFib	skin:	n/a
5	chr1:153914492-153914542	RPTEC	kidney:	n/a
6	chr1:153914453-153914503	H1-hESC	embryonic stem cell:	embryo
7	chr1:153914492-153914542	HCF	heart:	n/a
8	chr1:153914453-153914503	HNPCEpiC	eye:	n/a
9	chr1:153914492-153914542	HRPEpiC	eye:	n/a
10	chr1:153914492-153914542	NB4	blood:	n/a
11	chr1:153914492-153914542	HIPEpiC	eye:	n/a
12	chr1:153914453-153914503	SKMC	muscle:	n/a
13	chr1:153914492-153914542	AG09319	gingival:	n/a
14	chr1:153914453-153914503	BJ	skin:	n/a
15	chr1:153914492-153914542	GM06990	blood:	n/a
16	chr1:153914492-153914542	SK-N-SH_RA	brain:	n/a
17	chr1:153914492-153914542	AG10803	skin:	n/a
18	chr1:153914492-153914542	HCT-116	colon:	n/a
19	chr1:153914453-153914503	NHDF-neo	bronchial:	n/a
20	chr1:153914453-153914503	NHBE	bronchial:	n/a
21	chr1:153914453-153914503	SAEC	small airway:	n/a
22	chr1:153914492-153914542	SK-N-SH	brain:	n/a
23	chr1:153914453-153914503	HIPEpiC	eye:	n/a
24	chr1:153914492-153914542	BE2_C	brain:	n/a
25	chr1:153914492-153914542	GM19239	blood:	n/a
26	chr1:153914492-153914542	NHBE	bronchial:	n/a
27	chr1:153914453-153914503	ovcar-3	ovarian:	n/a
28	chr1:153914453-153914503	CMK	blood:	n/a
29	chr1:153914492-153914542	CMK	blood:	n/a
30	chr1:153914453-153914503	U87	brain:	n/a
31	chr1:153914492-153914542	IMR90	lung:	fetal
32	chr1:153914453-153914503	AG09319	gingival:	n/a
33	chr1:153914492-153914542	SAEC	small airway:	n/a
34	chr1:153914453-153914503	Hepatocyte	liver:	n/a
35	chr1:153914453-153914503	HRE	kidney:	n/a
36	chr1:153914492-153914542	Jurkat	blood:	n/a
37	chr1:153914453-153914503	HCM	heart:	n/a
38	chr1:153914453-153914503	BE2_C	brain:	n/a
39	chr1:153914453-153914503	GM12891	blood:	n/a
40	chr1:153914492-153914542	ECC-1	luminal epithelium:	n/a
41	chr1:153914492-153914542	AG04449	skin:	fetal
42	chr1:153914492-153914542	HPAEpiC	pulmonary alveolar:	n/a
43	chr1:153914492-153914542	SK-N-MC	brain:	n/a
44	chr1:153914453-153914503	PANC-1	pancreas:	n/a
45	chr1:153914492-153914542	ovcar-3	ovarian:	n/a
46	chr1:153914453-153914503	AG04450	lung:	fetal
47	chr1:153914453-153914503	PFSK-1	brain:	n/a
48	chr1:153914453-153914503	HRCEpiC	kidney:	n/a
49	chr1:153914453-153914503	Caco-2	colon:	n/a
50	chr1:153914492-153914542	Hepatocyte	liver:	n/a

No data

Variant related genes	Relation type
DENND4B	TF binding region
DENND4B	CpG island

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10908488	0.80[AFR][1000 genomes]
rs4489596	0.88[AFR][1000 genomes]
rs4845582	0.86[AFR][1000 genomes]
rs6673803	0.93[AFR][1000 genomes]
rs74115717	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7526877	0.87[AFR][1000 genomes]
rs7528635	0.95[AFR][1000 genomes]
rs9427245	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv872450	chr1:153889042-153937513	Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 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	chr1:153896800-153917600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:153897000-153916400	Weak transcription	Fetal Brain Male	brain
3	chr1:153897400-153916600	Weak transcription	Fetal Heart	heart
4	chr1:153901000-153915400	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:153901000-153915600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:153901000-153916400	Strong transcription	Fetal Thymus	thymus
7	chr1:153901200-153914800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:153901200-153915600	Strong transcription	Primary T cells from cord blood	blood
9	chr1:153901400-153914800	Strong transcription	Primary B cells from cord blood	blood
10	chr1:153901400-153915800	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr1:153901400-153915800	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:153901400-153916400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:153901400-153916400	Strong transcription	Brain Germinal Matrix	brain
14	chr1:153901400-153916400	Strong transcription	Fetal Intestine Large	intestine
15	chr1:153901400-153916600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:153901400-153916600	Strong transcription	Fetal Stomach	stomach
17	chr1:153901400-153916800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:153901400-153916800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:153901400-153917200	Strong transcription	Fetal Intestine Small	intestine
20	chr1:153901600-153915200	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:153901600-153915800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:153901600-153915800	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr1:153901600-153916200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:153901600-153916200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:153901600-153916600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:153901600-153916600	Strong transcription	Thymus	Thymus
27	chr1:153901600-153916800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:153901600-153916800	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:153901600-153917000	Strong transcription	Fetal Brain Female	brain
30	chr1:153901800-153915200	Strong transcription	Liver	Liver
31	chr1:153901800-153916400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:153901800-153917000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:153902000-153914800	Strong transcription	Spleen	Spleen
34	chr1:153902000-153915000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:153902000-153915400	Strong transcription	Placenta	Placenta
36	chr1:153902000-153915600	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:153902000-153915600	Strong transcription	GM12878-XiMat	blood
38	chr1:153902000-153915800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:153902000-153915800	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr1:153902000-153916400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:153902000-153916600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:153902000-153916600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:153902000-153916600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:153902000-153917000	Strong transcription	NHLF	lung
45	chr1:153902200-153915600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:153902200-153916600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:153902400-153915200	Strong transcription	Right Ventricle	heart
48	chr1:153902400-153916400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:153902400-153916400	Strong transcription	Dnd41	blood
50	chr1:153902400-153916600	Strong transcription	Ovary	ovary

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