Variant report

Variant	rs7689569
Chromosome Location	chr4:55096398-55096399
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	MXI1	chr4:55093006-55098852	SK-N-SH	brain:	n/a	n/a
2	MXI1	chr4:55092563-55098831	IMR90	lung:	n/a	n/a
3	SIN3A	chr4:55096357-55096580	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr4:55096304-55096761	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr4:55096300-55096450	SK-N-SH_RA	brain:	n/a	n/a
6	CHD1	chr4:55092095-55098811	IMR90	lung:	n/a	chr4:55095204-55095214 chr4:55097509-55097519 chr4:55092863-55092873
7	MAZ	chr4:55092981-55097889	IMR90	lung:	n/a	chr4:55096617-55096627 chr4:55095167-55095177 chr4:55096597-55096607 chr4:55094630-55094639 chr4:55096994-55097003
8	TEAD4	chr4:55096353-55096753	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTBP2	chr4:55096280-55098331	H1-hESC	embryonic stem cell:	n/a	n/a
10	SUZ12	chr4:55095519-55098756	NT2-D1	testis:	n/a	n/a
11	SMC3	chr4:55092553-55098497	SK-N-SH	brain:	n/a	chr4:55094171-55094179 chr4:55098142-55098152
12	MAX	chr4:55096112-55096503	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55094459..55096231-chr4:55096303..55097882,2	K562	blood:

Variant related genes	Relation type
PDGFRA	TF binding region
ENSG00000134853	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11133315	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12505491	0.81[ASN][1000 genomes]
rs12506290	0.81[ASN][1000 genomes]
rs12508225	0.81[ASN][1000 genomes]
rs12641563	0.81[ASN][1000 genomes]
rs12644709	0.81[ASN][1000 genomes]
rs12644749	0.81[ASN][1000 genomes]
rs1565669	0.81[ASN][1000 genomes]
rs1565670	0.81[ASN][1000 genomes]
rs17084051	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800809	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800810	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800812	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800813	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229307	0.81[ASN][1000 genomes]
rs2307049	0.81[ASN][1000 genomes]
rs28489067	0.80[ASN][1000 genomes]
rs28528897	0.81[ASN][1000 genomes]
rs28600756	0.81[ASN][1000 genomes]
rs4358459	0.81[ASN][1000 genomes]
rs4368668	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4422471	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4608869	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4635872	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864857	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864858	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864859	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864860	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864861	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864862	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864863	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864864	0.81[ASN][1000 genomes]
rs4864865	0.81[ASN][1000 genomes]
rs56145315	0.81[ASN][1000 genomes]
rs58435984	0.85[ASN][1000 genomes]
rs58727676	0.81[ASN][1000 genomes]
rs60806423	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60863210	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61320297	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554158	0.85[AFR][1000 genomes]
rs6554160	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67279506	0.81[ASN][1000 genomes]
rs67432867	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67600360	0.81[ASN][1000 genomes]
rs6831380	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6832597	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6836215	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850748	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73252942	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73252946	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73252948	0.81[ASN][1000 genomes]
rs7660560	0.81[ASN][1000 genomes]
rs7673027	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673597	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673625	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673853	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673984	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676972	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7677751	0.95[ASN][1000 genomes]
rs7678144	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7679903	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681399	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682912	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7686588	0.81[ASN][1000 genomes]
rs7688997	0.81[ASN][1000 genomes]
rs7690503	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691129	0.81[ASN][1000 genomes]
rs7698425	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890203	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991165	0.84[AMR][1000 genomes];0.86[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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