Variant report

Variant	rs13020999
Chromosome Location	chr2:190003488-190003489
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10165127	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10165257	0.92[EUR][1000 genomes]
rs1016622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931401	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10931411	0.82[EUR][1000 genomes]
rs11681286	0.80[AFR][1000 genomes]
rs11901914	0.95[EUR][1000 genomes]
rs12104769	0.80[AFR][1000 genomes]
rs12618316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999996	0.80[AFR][1000 genomes]
rs13005652	0.82[AFR][1000 genomes]
rs13005714	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13005834	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13006065	0.92[EUR][1000 genomes]
rs13013089	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017413	0.80[AFR][1000 genomes]
rs13019651	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13024858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13028967	0.80[AFR][1000 genomes]
rs13030984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13033421	0.81[AFR][1000 genomes]
rs1356162	0.82[AFR][1000 genomes]
rs1356163	0.82[AFR][1000 genomes]
rs1356164	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs1464135	1.00[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1515864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1515869	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533618	0.88[EUR][1000 genomes]
rs1949327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965422	0.83[YRI][hapmap]
rs2138373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138374	0.87[YRI][hapmap]
rs36019389	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4428040	0.83[AFR][1000 genomes]
rs4667263	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667265	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs4667266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4667268	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4667271	0.88[EUR][1000 genomes]
rs4667275	0.82[EUR][1000 genomes]
rs4998559	0.84[YRI][hapmap]
rs62182416	0.81[AFR][1000 genomes]
rs62182417	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6434325	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708419	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs6714088	0.82[AFR][1000 genomes]
rs6719104	0.82[AFR][1000 genomes]
rs6730236	0.92[CHB][hapmap]
rs6741804	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6749559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6752781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561002	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs7593860	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599222	0.88[EUR][1000 genomes]
rs7606337	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13020999	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189968600-190012000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:189974800-190007600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:189981400-190014800	Weak transcription	Fetal Stomach	stomach
4	chr2:189982400-190005800	Weak transcription	Fetal Kidney	kidney
5	chr2:189984000-190016800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:189986000-190008800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:189993800-190007400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:189993800-190017000	Weak transcription	Ovary	ovary
9	chr2:189994200-190010600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:189995400-190009000	Weak transcription	Adipose Nuclei	Adipose
11	chr2:189996000-190008800	Weak transcription	NHLF	lung
12	chr2:189997000-190008000	Weak transcription	HSMMtube	muscle
13	chr2:189997000-190008600	Weak transcription	NH-A	brain
14	chr2:189998800-190005800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:189999000-190009400	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:189999200-190003800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:190000400-190013600	Weak transcription	Left Ventricle	heart
18	chr2:190001000-190008000	Weak transcription	Fetal Lung	lung
19	chr2:190002400-190008400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:190002600-190003600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:190002600-190003800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:190002600-190004400	Strong transcription	HSMM	muscle
23	chr2:190002600-190007800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:190002600-190007800	Weak transcription	NHDF-Ad	bronchial
25	chr2:190002600-190009000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:190002800-190008800	Weak transcription	Osteobl	bone
27	chr2:190003000-190003600	Enhancers	Colon Smooth Muscle	Colon
28	chr2:190003000-190004400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:190003000-190008800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:190003200-190004000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:190003200-190006000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:190003400-190003600	Flanking Active TSS	A549	lung
33	chr2:190003400-190004000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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