Variant report

Variant	rs2366858
Chromosome Location	chr7:80340622-80340623
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10499863	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10808255	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11770916	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12670520	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1358338	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1358339	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1405746	0.95[AFR][1000 genomes]
rs1527466	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1527469	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1527471	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1527473	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1527474	1.00[AMR][1000 genomes]
rs1609151	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1918371	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1918372	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1918373	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1918374	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1918375	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1949970	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1949971	1.00[MEX][hapmap]
rs2222713	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2886791	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3211892	1.00[MEX][hapmap]
rs41486545	1.00[MEX][hapmap]
rs6467337	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6467363	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6467371	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs6958853	1.00[AMR][1000 genomes]
rs6958863	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6963015	0.92[AFR][1000 genomes]
rs6969280	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9641897	0.92[AFR][1000 genomes];1.00[AMR][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	nsv888524	chr7:80107798-80723062	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv888526	chr7:80240943-80354229	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HDL cholesterol	23726366	GWAS catalog

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80336800-80340800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr7:80337200-80340800	Weak transcription	NHLF	lung
3	chr7:80337200-80341200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:80339800-80340800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr7:80339800-80341000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:80339800-80341000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr7:80340400-80340800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:80340400-80341000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:80340400-80341400	Enhancers	NHDF-Ad	bronchial
10	chr7:80340600-80341400	Enhancers	Osteobl	bone

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