Variant report

Variant	rs1520858
Chromosome Location	chr2:190271533-190271534
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10166420	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10175108	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10188246	0.84[ASN][1000 genomes]
rs10198663	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10207812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10210634	0.98[ASN][1000 genomes]
rs10804029	0.90[ASN][1000 genomes]
rs10931411	0.84[EUR][1000 genomes]
rs10931417	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11676905	0.84[ASN][1000 genomes]
rs11677167	0.98[ASN][1000 genomes]
rs11678414	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12613903	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12622720	0.83[ASN][1000 genomes]
rs12623394	0.80[ASN][1000 genomes]
rs12693539	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693540	0.83[ASN][1000 genomes]
rs12994482	0.84[ASN][1000 genomes]
rs13009912	0.87[ASN][1000 genomes]
rs13015207	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13018252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13035381	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1356976	1.00[ASN][1000 genomes]
rs1520854	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520856	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520866	0.85[ASN][1000 genomes]
rs1595749	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16831454	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1851104	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1866605	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1898971	0.83[ASN][1000 genomes]
rs1992295	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304702	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2351932	0.86[ASN][1000 genomes]
rs2351934	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2683012	0.86[ASN][1000 genomes]
rs2882805	0.92[ASN][1000 genomes]
rs4309611	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4580411	0.95[ASN][1000 genomes]
rs4666775	0.89[ASN][1000 genomes]
rs4667275	0.84[EUR][1000 genomes]
rs4667280	0.96[ASN][1000 genomes]
rs4667284	0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6434340	0.95[ASN][1000 genomes]
rs6434342	0.93[ASN][1000 genomes]
rs6434343	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6738193	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6747222	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6752545	0.98[ASN][1000 genomes]
rs734859	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7420765	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7422875	0.84[ASN][1000 genomes]
rs7425383	0.84[ASN][1000 genomes]
rs744556	0.80[ASN][1000 genomes]
rs745742	0.83[ASN][1000 genomes]
rs7556928	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7566093	0.98[ASN][1000 genomes]
rs7574403	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7590098	0.85[AMR][1000 genomes]
rs8179541	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8179732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs893407	0.83[ASN][1000 genomes]
rs893408	0.80[ASN][1000 genomes]
rs9677436	0.93[AFR][1000 genomes];0.98[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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1520858	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190258800-190272000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:190258800-190272600	Weak transcription	Aorta	Aorta
3	chr2:190268000-190272400	Weak transcription	NHEK	skin
4	chr2:190268200-190272400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:190268200-190276800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:190269200-190275000	Weak transcription	Fetal Intestine Small	intestine
7	chr2:190269800-190271600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:190270400-190274400	Enhancers	Rectal Smooth Muscle	rectum
9	chr2:190271000-190272000	Enhancers	NHLF	lung
10	chr2:190271200-190271600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:190271200-190271800	Enhancers	A549	lung
12	chr2:190271200-190272000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:190271200-190272000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:190271200-190272000	Enhancers	NHDF-Ad	bronchial
15	chr2:190271200-190272000	Enhancers	Osteobl	bone
16	chr2:190271200-190272200	Enhancers	Colon Smooth Muscle	Colon
17	chr2:190271200-190272600	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr2:190271200-190273200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:190271200-190273200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr2:190271400-190271600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:190271400-190272000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:190271400-190272000	Enhancers	NH-A	brain
23	chr2:190271400-190272200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr2:190271400-190272200	Enhancers	HSMM	muscle
25	chr2:190271400-190272400	Enhancers	HUVEC	blood vessel
26	chr2:190271400-190273200	Enhancers	Fetal Lung	lung
27	chr2:190271400-190273200	Enhancers	HMEC	breast
28	chr2:190271400-190274200	Enhancers	Fetal Stomach	stomach

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