Variant report

Variant	rs6860626
Chromosome Location	chr5:59636727-59636728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10461451	0.81[AFR][1000 genomes]
rs12653863	0.81[AFR][1000 genomes]
rs13165296	0.92[EUR][1000 genomes]
rs13168619	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13171028	0.81[AFR][1000 genomes]
rs13172481	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34038162	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34353877	0.81[AFR][1000 genomes]
rs35335033	0.89[EUR][1000 genomes]
rs35644384	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35811820	0.81[AFR][1000 genomes]
rs35914313	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36050835	0.81[AFR][1000 genomes]
rs4349679	0.81[AFR][1000 genomes]
rs4394088	0.81[AFR][1000 genomes]
rs4502776	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4699954	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56341652	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57237852	0.83[AFR][1000 genomes]
rs6449468	0.81[AFR][1000 genomes]
rs6861084	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6862735	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6869495	0.89[EUR][1000 genomes]
rs71630006	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7706560	0.92[EUR][1000 genomes]
rs7733705	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59625200-59646800	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59632600-59637200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:59635200-59637400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr5:59635200-59638600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:59635400-59637200	Enhancers	Brain Cingulate Gyrus	brain
6	chr5:59635400-59637400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr5:59635800-59637600	Enhancers	GM12878-XiMat	blood
8	chr5:59635800-59639200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:59636000-59637000	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:59636000-59637200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:59636000-59637200	Weak transcription	Aorta	Aorta
12	chr5:59636000-59637200	Enhancers	Brain Substantia Nigra	brain
13	chr5:59636000-59637400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:59636000-59637400	Enhancers	Brain Hippocampus Middle	brain
15	chr5:59636000-59637400	Enhancers	Fetal Brain Female	brain
16	chr5:59636000-59637800	Enhancers	Fetal Brain Male	brain
17	chr5:59636200-59637000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:59636200-59637000	Enhancers	Osteobl	bone
19	chr5:59636400-59637000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:59636600-59637400	Enhancers	NHDF-Ad	bronchial
21	chr5:59636600-59637800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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