Variant report

Variant	rs2408227
Chromosome Location	chr5:124308088-124308089
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10044837	0.80[ASN][1000 genomes]
rs1112727	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12515229	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12515871	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1961388	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2166410	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2166411	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2408229	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2408231	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34105150	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35689682	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35879477	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36088659	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4441872	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4835849	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4835850	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62372816	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62372824	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6861554	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6868443	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6868598	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875807	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6876737	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6890814	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73782560	0.80[AMR][1000 genomes]
rs7444060	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7701094	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[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	nsv882822	chr5:124250018-124449375	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830474	chr5:124263628-124431299	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv599657	chr5:124284253-124330522	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124300000-124311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:124302600-124309600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:124303000-124309600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:124304400-124309000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:124306400-124308600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:124306800-124308600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:124306800-124308800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:124307200-124310000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr5:124307600-124310200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr5:124307800-124308800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:124307800-124308800	Enhancers	Adipose Nuclei	Adipose
12	chr5:124307800-124309000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:124308000-124308400	Enhancers	Brain Germinal Matrix	brain
14	chr5:124308000-124309200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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