Variant report

Variant	rs2589506
Chromosome Location	chr4:86939692-86939693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:86932598..86934396-chr4:86939558..86941461,2	MCF-7	breast:
2	chr4:86933270..86935055-chr4:86936823..86940226,3	K562	blood:

Variant related genes	Relation type
ENSG00000261496	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12502934	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12512583	0.89[ASN][1000 genomes]
rs13103374	0.96[ASN][1000 genomes]
rs13112959	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13353771	0.93[ASN][1000 genomes]
rs1469869	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1898248	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1898249	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1946733	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2118044	0.93[ASN][1000 genomes]
rs2282596	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2282597	0.96[ASN][1000 genomes]
rs2282598	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2575675	0.87[CHD][hapmap]
rs2589514	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589516	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	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];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]
rs7699978	0.87[CHD][hapmap]
rs9307015	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs958	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9884282	0.95[CHB][hapmap];0.80[CHD][hapmap];0.85[ASN][1000 genomes]
rs9884770	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9995879	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];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:28 , 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	chr4:86928600-86953400	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:86932800-86953800	Weak transcription	Fetal Lung	lung
7	chr4:86933400-86940200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:86934200-86942200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:86934200-86953400	Weak transcription	Aorta	Aorta
10	chr4:86935200-86942200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:86935200-86949200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:86936000-86948000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:86936000-86975600	Weak transcription	Brain Germinal Matrix	brain
14	chr4:86936200-86940200	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:86936400-86954600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:86936400-86990600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:86936600-86948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:86936800-86953600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:86938200-86954200	Weak transcription	Fetal Kidney	kidney
20	chr4:86938400-86953400	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:86938600-86940400	Weak transcription	Brain Anterior Caudate	brain
22	chr4:86938600-86945800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:86938600-86949000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:86938600-86953400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:86938600-86953600	Weak transcription	Brain Angular Gyrus	brain
26	chr4:86938600-86954000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:86938600-86957800	Weak transcription	Fetal Brain Female	brain
28	chr4:86939200-86953800	Weak transcription	Fetal Stomach	stomach

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