Variant report

Variant	rs599583
Chromosome Location	chr1:78905940-78905941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10489786	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs11162483	1.00[YRI][hapmap]
rs1156032	0.90[AFR][1000 genomes]
rs1265657	1.00[AMR][1000 genomes]
rs1265663	1.00[AMR][1000 genomes]
rs1322930	1.00[AMR][1000 genomes]
rs1322932	1.00[AMR][1000 genomes]
rs1322936	1.00[AMR][1000 genomes]
rs1332255	0.89[AFR][1000 genomes]
rs1332256	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs1333979	1.00[AMR][1000 genomes]
rs1412846	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17101751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17101783	1.00[AMR][1000 genomes]
rs1888894	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs1888895	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs1888896	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs2149032	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs4650347	0.81[YRI][hapmap];0.96[AFR][1000 genomes]
rs487376	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs494131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs540676	0.83[YRI][hapmap]
rs553310	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs559854	1.00[AMR][1000 genomes]
rs564407	0.80[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs569846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs574426	0.86[AFR][1000 genomes]
rs576056	0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs581338	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs601137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs602865	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs626770	1.00[AFR][1000 genomes]
rs640003	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6424768	0.94[AFR][1000 genomes]
rs6424769	0.98[AFR][1000 genomes]
rs645528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs663485	1.00[AMR][1000 genomes]
rs664465	0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs676130	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs689110	1.00[AMR][1000 genomes]
rs7516567	1.00[AMR][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	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv482697	chr1:78786028-78935333	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv870807	chr1:78867347-79032598	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78903800-78913000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:78904800-78907800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:78905000-78906800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:78905400-78906200	Enhancers	Hela-S3	cervix
5	chr1:78905400-78908400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:78905600-78906200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:78905600-78906200	Enhancers	NHDF-Ad	bronchial
8	chr1:78905600-78906200	Enhancers	Osteobl	bone
9	chr1:78905800-78906000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:78905800-78906000	Enhancers	Fetal Muscle Leg	muscle
11	chr1:78905800-78906000	Enhancers	HSMMtube	muscle
12	chr1:78905800-78906800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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