Variant report

Variant	rs2408229
Chromosome Location	chr5:124301976-124301977
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1112727	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515229	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12515871	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12517390	0.82[ASN][1000 genomes]
rs1961388	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028855	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2166410	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2166411	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2408227	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2408231	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34105150	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35649581	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35689682	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35879477	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36088659	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4441872	0.90[ASN][1000 genomes]
rs4835849	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4835850	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4836129	0.82[ASN][1000 genomes]
rs4836130	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62372816	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62372824	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6861554	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6868443	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6868598	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6875807	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6876737	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6890814	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7444060	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7701094	0.80[AMR][1000 genomes];0.90[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:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124299000-124306800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:124299600-124302000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:124300000-124305600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:124300000-124306800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:124300000-124311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:124300200-124302000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:124300200-124302000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:124301200-124302000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:124301800-124302200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr5:124301800-124302400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr5:124301800-124302400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:124301800-124302400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr5:124301800-124302400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr5:124301800-124302600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr5:124301800-124303000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr5:124301800-124304600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links