Variant report

Variant	rs13003020
Chromosome Location	chr2:55407610-55407611
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10496038	0.89[CEU][hapmap]
rs1134722	0.89[EUR][1000 genomes]
rs11686766	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11686912	0.89[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11687876	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12989854	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12995548	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13000786	0.89[EUR][1000 genomes]
rs13012567	0.89[EUR][1000 genomes]
rs13014752	0.95[EUR][1000 genomes]
rs13017468	1.00[CEU][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs13032294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2028139	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34447956	0.89[EUR][1000 genomes]
rs35141050	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35183885	1.00[CEU][hapmap];0.82[YRI][hapmap];0.97[EUR][1000 genomes]
rs35227659	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35700883	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36121000	0.89[EUR][1000 genomes]
rs4318424	0.89[CEU][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4627623	0.81[EUR][1000 genomes]
rs6730950	0.84[JPT][hapmap]
rs6742306	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6743339	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6747466	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71414544	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71414545	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71414546	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71414547	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71414548	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71414549	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71414556	0.94[EUR][1000 genomes]
rs71414557	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
2	chr2:55393000-55422000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:55394000-55419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:55395600-55412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:55395600-55422800	Weak transcription	Ovary	ovary
6	chr2:55395600-55427000	Weak transcription	Left Ventricle	heart
7	chr2:55395800-55418200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:55395800-55418400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:55395800-55427000	Weak transcription	Aorta	Aorta
10	chr2:55397000-55410000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:55397200-55450000	Weak transcription	NH-A	brain
12	chr2:55397400-55411600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:55397400-55422400	Weak transcription	HSMMtube	muscle
14	chr2:55397400-55423000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:55399600-55419000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:55399600-55423000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:55399800-55416600	Weak transcription	Primary T cells from cord blood	blood
18	chr2:55401000-55409000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:55401600-55419000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:55401800-55409000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:55402600-55422000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:55402600-55423200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
24	chr2:55403200-55408800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:55403200-55409400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:55403200-55423800	Weak transcription	Osteobl	bone
27	chr2:55403200-55426800	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:55403200-55431800	Weak transcription	Fetal Brain Male	brain
29	chr2:55403400-55418800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:55403400-55423000	Weak transcription	NHEK	skin
31	chr2:55403600-55416600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:55403600-55420600	Weak transcription	HSMM	muscle
33	chr2:55404200-55423000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:55405400-55423000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:55406800-55423000	Weak transcription	Lung	lung
36	chr2:55407400-55408200	Enhancers	HepG2	liver

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