Variant report

Variant	rs17275950
Chromosome Location	chr3:59523054-59523055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11130714	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11923741	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12486826	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12487257	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489949	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12492287	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12492308	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12493195	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17275189	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17275985	0.81[AMR][1000 genomes]
rs4679487	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56197311	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57042572	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58664036	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73837348	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73837355	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9855650	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011181	chr3:58665373-59542339	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv536574	chr3:58665373-59542339	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv534257	chr3:58855959-59606464	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv876836	chr3:59500394-59664687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17275950	HESX1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59508200-59526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:59517600-59524800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:59518000-59530800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:59518600-59524400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:59522200-59523400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:59522200-59525600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:59522200-59525600	Weak transcription	NH-A	brain
8	chr3:59522200-59526000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:59522200-59526400	Weak transcription	HSMM	muscle
10	chr3:59522400-59524800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:59522400-59525000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:59522400-59525600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:59522800-59525000	Weak transcription	Osteobl	bone
14	chr3:59522800-59525400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:59523000-59525800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:59523000-59528000	Weak transcription	Fetal Heart	heart

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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