Variant report

Variant	rs2548413
Chromosome Location	chr5:96521988-96521989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10040634	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs10045981	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs10055532	0.81[ASN][1000 genomes]
rs10057166	0.81[ASN][1000 genomes]
rs10075312	0.81[ASN][1000 genomes]
rs10476700	0.81[ASN][1000 genomes]
rs11135494	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs12516613	1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs12519482	0.80[ASN][1000 genomes]
rs12653352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12657849	0.81[ASN][1000 genomes]
rs167590	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs172741	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548417	0.80[ASN][1000 genomes]
rs2548418	0.80[ASN][1000 genomes]
rs317111	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7709067	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs9918187	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv830412	chr5:96427305-96606619	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1019790	chr5:96471680-96980633	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv537812	chr5:96471680-96980633	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv882391	chr5:96496189-96533469	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv882392	chr5:96496189-96546238	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv882393	chr5:96496189-96567950	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96519200-96526200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:96520000-96522800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:96520000-96523200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:96520000-96528200	Weak transcription	NHEK	skin
5	chr5:96520000-96531600	Weak transcription	HSMM	muscle
6	chr5:96520000-96534800	Weak transcription	Left Ventricle	heart
7	chr5:96520200-96523200	Weak transcription	Lung	lung
8	chr5:96520200-96524600	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:96520200-96524800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:96521000-96524400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:96521400-96522800	Strong transcription	Primary B cells from cord blood	blood
12	chr5:96521600-96523200	Enhancers	Dnd41	blood
13	chr5:96521600-96530000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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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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