Variant report

Variant	rs7668190
Chromosome Location	chr4:55096270-55096271
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr4:55093006-55098852	SK-N-SH	brain:	n/a	n/a
2	MXI1	chr4:55092563-55098831	IMR90	lung:	n/a	n/a
3	CHD1	chr4:55092095-55098811	IMR90	lung:	n/a	chr4:55095204-55095214 chr4:55097509-55097519 chr4:55092863-55092873
4	MAZ	chr4:55092981-55097889	IMR90	lung:	n/a	chr4:55096617-55096627 chr4:55095167-55095177 chr4:55096597-55096607 chr4:55094630-55094639 chr4:55096994-55097003
5	SUZ12	chr4:55095519-55098756	NT2-D1	testis:	n/a	n/a
6	SMC3	chr4:55092553-55098497	SK-N-SH	brain:	n/a	chr4:55094171-55094179 chr4:55098142-55098152
7	MAX	chr4:55096112-55096503	SK-N-SH	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:55096230-55096280	HCT-116	colon:	n/a
2	chr4:55096230-55096280	NHDF-neo	bronchial:	n/a
3	chr4:55096230-55096280	NH-A	brain:	n/a
4	chr4:55096230-55096280	SK-N-MC	brain:	n/a
5	chr4:55096230-55096280	SK-N-SH	brain:	n/a
6	chr4:55096230-55096280	NB4	blood:	n/a
7	chr4:55096230-55096280	HAEpiC	amniotic membrane:	n/a
8	chr4:55096230-55096280	SK-N-SH_RA	brain:	n/a
9	chr4:55096230-55096280	AoSMC	blood vessel:	n/a
10	chr4:55096230-55096280	PrEC	prostate:	n/a
11	chr4:55096230-55096280	HMEC	breast:	n/a
12	chr4:55096230-55096280	HNPCEpiC	eye:	n/a
13	chr4:55096230-55096280	Hepatocyte	liver:	n/a
14	chr4:55096230-55096280	MCF10A-Er-Src	breast:	n/a
15	chr4:55096230-55096280	BE2_C	brain:	n/a
16	chr4:55096230-55096280	IMR90	lung:	fetal
17	chr4:55096230-55096280	ECC-1	luminal epithelium:	n/a
18	chr4:55096230-55096280	HL-60	blood:	n/a
19	chr4:55096230-55096280	GM12878	blood:	n/a
20	chr4:55096230-55096280	HUVEC	blood vessel:	n/a
21	chr4:55096230-55096280	NHBE	bronchial:	n/a
22	chr4:55096230-55096280	HCF	heart:	n/a
23	chr4:55096230-55096280	SAEC	small airway:	n/a
24	chr4:55096230-55096280	ovcar-3	ovarian:	n/a
25	chr4:55096230-55096280	AG09309	skin:	n/a
26	chr4:55096230-55096280	T-47D	breast:	n/a
27	chr4:55096230-55096280	CMK	blood:	n/a
28	chr4:55096230-55096280	ProgFib	skin:	n/a
29	chr4:55096230-55096280	PANC-1	pancreas:	n/a
30	chr4:55096230-55096280	HRE	kidney:	n/a
31	chr4:55096230-55096280	SKMC	muscle:	n/a
32	chr4:55096230-55096280	HPAEpiC	pulmonary alveolar:	n/a
33	chr4:55096230-55096280	RPTEC	kidney:	n/a
34	chr4:55096230-55096280	Hela-S3	cervix:	n/a
35	chr4:55096230-55096280	PFSK-1	brain:	n/a
36	chr4:55096230-55096280	HIPEpiC	eye:	n/a
37	chr4:55096230-55096280	HCPEpiC	choroid plexus:	n/a
38	chr4:55096230-55096280	MCF-7	breast:	n/a
39	chr4:55096230-55096280	GM12891	blood:	n/a
40	chr4:55096230-55096280	HCM	heart:	n/a
41	chr4:55096230-55096280	GM19239	blood:	n/a
42	chr4:55096230-55096280	Caco-2	colon:	n/a
43	chr4:55096230-55096280	AG09319	gingival:	n/a
44	chr4:55096230-55096280	GM12892	blood:	n/a
45	chr4:55096230-55096280	AG10803	skin:	n/a
46	chr4:55096230-55096280	HRCEpiC	kidney:	n/a
47	chr4:55096230-55096280	U87	brain:	n/a
48	chr4:55096230-55096280	Jurkat	blood:	n/a
49	chr4:55096230-55096280	HepG2	liver:	n/a
50	chr4:55096230-55096280	HEK293	kidney:	embryo

No data

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

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13435164	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2114039	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28622224	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864504	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554162	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554164	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6554165	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002905	chr4:55093677-55115698	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55091200-55099000	Bivalent/Poised TSS	Fetal Kidney	kidney
2	chr4:55091400-55096600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
3	chr4:55092000-55096800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr4:55092000-55100800	Active TSS	Aorta	Aorta
5	chr4:55092400-55097800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr4:55092400-55100600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:55093200-55100800	Active TSS	NHDF-Ad	bronchial
8	chr4:55093200-55102000	Active TSS	Ovary	ovary
9	chr4:55093800-55096400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:55093800-55097000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr4:55093800-55097800	Bivalent/Poised TSS	Fetal Lung	lung
12	chr4:55094200-55099000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
13	chr4:55094200-55100800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:55094400-55097000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:55094400-55098000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
16	chr4:55094400-55098600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:55094600-55096400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:55094600-55096600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:55094600-55096600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:55094600-55096800	Bivalent/Poised TSS	Fetal Stomach	stomach
21	chr4:55094600-55097000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
22	chr4:55094600-55097200	Active TSS	Right Atrium	heart
23	chr4:55094600-55097800	Bivalent Enhancer	HUVEC	blood vessel
24	chr4:55094600-55098000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
25	chr4:55094600-55098200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
26	chr4:55094800-55096400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
27	chr4:55094800-55096600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:55094800-55096600	Active TSS	NHLF	lung
29	chr4:55094800-55096800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
30	chr4:55094800-55100800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:55095000-55096400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
32	chr4:55095000-55096400	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
33	chr4:55095000-55096800	Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr4:55095000-55097000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr4:55095000-55097800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
36	chr4:55095000-55100400	Active TSS	Osteobl	bone
37	chr4:55095000-55100600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:55095000-55100800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
39	chr4:55095200-55098800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:55095400-55096800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
41	chr4:55095400-55097000	Bivalent/Poised TSS	Left Ventricle	heart
42	chr4:55095600-55099400	Bivalent/Poised TSS	Psoas Muscle	Psoas
43	chr4:55095600-55100600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
44	chr4:55095800-55096400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:55095800-55096400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
46	chr4:55095800-55098600	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
47	chr4:55095800-55098600	Bivalent/Poised TSS	Small Intestine	intestine
48	chr4:55096000-55096400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr4:55096000-55096400	Bivalent Enhancer	Fetal Brain Male	brain
50	chr4:55096000-55097200	Bivalent Enhancer	Primary hematopoietic stem cells	blood

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