Variant report

Variant	rs6880992
Chromosome Location	chr5:146417295-146417296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10077240	0.85[CHB][hapmap]
rs10077327	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1031915	0.82[JPT][hapmap]
rs1031916	0.82[JPT][hapmap]
rs11167956	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1125457	0.83[JPT][hapmap]
rs11743368	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs12523317	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13165556	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs13183391	0.94[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1383167	0.92[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1383168	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs1480154	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs1842343	0.91[ASN][1000 genomes]
rs2054528	0.94[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2400234	0.86[ASN][1000 genomes]
rs2400236	0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2400241	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs61088380	0.83[ASN][1000 genomes]
rs62377581	0.86[ASN][1000 genomes]
rs62377606	0.80[EUR][1000 genomes]
rs6880660	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6881673	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs720303	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs922585	0.85[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9325031	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9325032	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs997979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1026599	chr5:146366481-146490089	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146401000-146418600	Weak transcription	Brain Anterior Caudate	brain
2	chr5:146401200-146418600	Weak transcription	Brain Hippocampus Middle	brain
3	chr5:146401200-146418600	Weak transcription	Brain Substantia Nigra	brain
4	chr5:146413200-146418400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:146413400-146418600	Weak transcription	Brain Angular Gyrus	brain
6	chr5:146413600-146418600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:146416200-146417800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:146416400-146417600	Enhancers	NH-A	brain
9	chr5:146416600-146417400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:146416600-146417800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:146416600-146417800	Enhancers	HMEC	breast
12	chr5:146416600-146418400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:146417000-146417600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:146417000-146418000	Enhancers	HSMM	muscle
15	chr5:146417200-146417600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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