Variant report

Variant	rs2589516
Chromosome Location	chr4:86937096-86937097
allele	G/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	GATA3	chr4:86936952-86937574	SK-N-SH	brain:	n/a	n/a
2	EBF1	chr4:86936981-86937125	GM12878	blood:	n/a	chr4:86937035-86937046
3	GATA2	chr4:86937090-86937565	SH-SY5Y	brain:	n/a	n/a
4	GATA3	chr4:86936961-86937527	SH-SY5Y	brain:	n/a	n/a
5	GATA3	chr4:86936939-86937553	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:86936705..86937415-chr4:86944933..86945745,2	MCF-7	breast:
2	chr4:86933270..86935055-chr4:86936823..86940226,3	K562	blood:

Variant related genes	Relation type
ENSG00000261496	TF binding region
ENSG00000261496	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10002407	0.96[ASN][1000 genomes]
rs10023731	0.89[ASN][1000 genomes]
rs10027225	0.85[ASN][1000 genomes]
rs10031752	0.90[ASN][1000 genomes]
rs11929863	0.92[ASN][1000 genomes]
rs1201	0.95[ASN][1000 genomes]
rs12502934	0.89[ASN][1000 genomes]
rs12512583	0.89[ASN][1000 genomes]
rs13103374	0.96[ASN][1000 genomes]
rs13112959	0.89[ASN][1000 genomes]
rs13353771	0.93[ASN][1000 genomes]
rs1469869	0.93[ASN][1000 genomes]
rs1898248	0.85[ASN][1000 genomes]
rs1898249	0.92[ASN][1000 genomes]
rs1946733	0.92[ASN][1000 genomes]
rs2118044	0.93[ASN][1000 genomes]
rs2282596	0.89[ASN][1000 genomes]
rs2282597	0.96[ASN][1000 genomes]
rs2282598	0.96[ASN][1000 genomes]
rs2589506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589514	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485608	0.85[ASN][1000 genomes]
rs28516651	0.88[ASN][1000 genomes]
rs28865277	0.96[ASN][1000 genomes]
rs34998174	0.85[ASN][1000 genomes]
rs35823399	0.89[ASN][1000 genomes]
rs3775167	0.96[ASN][1000 genomes]
rs3775170	0.96[ASN][1000 genomes]
rs3775184	0.90[ASN][1000 genomes]
rs4640664	0.83[AMR][1000 genomes]
rs6822410	0.81[ASN][1000 genomes]
rs6840318	0.93[ASN][1000 genomes]
rs9307015	0.92[ASN][1000 genomes]
rs958	0.96[ASN][1000 genomes]
rs9884282	0.85[ASN][1000 genomes]
rs9884770	0.89[ASN][1000 genomes]
rs9995879	0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86916800-86985400	Weak transcription	Ovary	ovary
2	chr4:86917000-86954000	Weak transcription	Pancreas	Pancrea
3	chr4:86917400-86940400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:86919400-86941200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:86925400-86937200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:86925600-86937400	Weak transcription	Fetal Kidney	kidney
7	chr4:86928400-86937800	Weak transcription	Fetal Stomach	stomach
8	chr4:86928600-86953400	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:86931600-86937600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:86931800-86937600	Enhancers	Osteobl	bone
11	chr4:86932400-86937600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:86932600-86937800	Weak transcription	Brain Angular Gyrus	brain
13	chr4:86932800-86953800	Weak transcription	Fetal Lung	lung
14	chr4:86933000-86937600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:86933400-86940200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:86934200-86942200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:86934200-86953400	Weak transcription	Aorta	Aorta
18	chr4:86934400-86937400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:86934400-86937800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr4:86935000-86937400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr4:86935000-86937600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:86935000-86937600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:86935200-86937400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:86935200-86942200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:86935200-86949200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:86935400-86937400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:86935400-86937600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:86935400-86938400	Weak transcription	Brain Substantia Nigra	brain
29	chr4:86935600-86938400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr4:86935800-86937400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr4:86935800-86937600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:86936000-86937200	Weak transcription	HSMM	muscle
33	chr4:86936000-86937800	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:86936000-86937800	Weak transcription	Fetal Brain Female	brain
35	chr4:86936000-86948000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:86936000-86975600	Weak transcription	Brain Germinal Matrix	brain
37	chr4:86936200-86937800	Weak transcription	Brain Anterior Caudate	brain
38	chr4:86936200-86937800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:86936200-86940200	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:86936400-86937400	Enhancers	NH-A	brain
41	chr4:86936400-86954600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:86936400-86990600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:86936600-86948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:86936800-86937800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr4:86936800-86953600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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