Variant report

Variant	rs27323
Chromosome Location	chr5:52552239-52552240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs152977	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs153119	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153120	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153121	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153126	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs166129	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs251505	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs251509	0.81[ASN][1000 genomes]
rs251512	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs251517	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs251580	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs254504	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs27316	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27324	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774234	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv830297	chr5:52492494-52707758	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv522454	chr5:52492677-52571758	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52541800-52559200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:52548200-52554400	Enhancers	NHEK	skin
3	chr5:52548600-52561400	Enhancers	HMEC	breast
4	chr5:52549800-52552800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:52550000-52552600	Weak transcription	HSMMtube	muscle
6	chr5:52550000-52558800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:52550200-52552400	Weak transcription	NH-A	brain
8	chr5:52550200-52552400	Weak transcription	Osteobl	bone
9	chr5:52550200-52552800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:52550200-52552800	Weak transcription	HSMM	muscle
11	chr5:52550200-52556600	Weak transcription	NHDF-Ad	bronchial
12	chr5:52550200-52556800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:52551200-52556400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:52551800-52554800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:52552000-52553000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:52552000-52553600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:52552200-52552400	Enhancers	NHLF	lung
18	chr5:52552200-52555600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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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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