Variant report

Variant	rs62404997
Chromosome Location	chr6:55788296-55788297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56665058	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61391371	0.93[EUR][1000 genomes]
rs62404993	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62404994	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62404996	0.89[EUR][1000 genomes]
rs62404998	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62404999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62405002	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405029	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405034	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405035	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405036	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405037	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405038	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405039	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405040	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405041	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405042	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405043	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405044	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405045	0.93[EUR][1000 genomes]
rs62406065	0.82[EUR][1000 genomes]
rs62406067	0.82[EUR][1000 genomes]
rs62406071	0.82[EUR][1000 genomes]
rs62406072	0.82[EUR][1000 genomes]
rs6936317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7740526	0.82[EUR][1000 genomes]
rs7748142	0.89[EUR][1000 genomes]
rs7770907	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9464305	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9475468	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9475474	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1024174	chr6:55713889-55829936	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1029301	chr6:55713889-55834480	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv830665	chr6:55755560-55920219	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv5312	chr6:55784991-55830051	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55783400-55789800	Weak transcription	NHEK	skin
2	chr6:55784200-55789600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:55784600-55789800	Weak transcription	Hela-S3	cervix
4	chr6:55784800-55789800	Weak transcription	HMEC	breast
5	chr6:55785000-55789000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links