Variant report

Variant	rs6881673
Chromosome Location	chr5:146421216-146421217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:17231434..17232256-chr5:146420463..146421464,6	HCT-116	colon:

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

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

rs_ID	r²[population]
rs10077240	0.83[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap]
rs10077327	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1031915	0.83[CEU][hapmap]
rs1031916	0.83[CEU][hapmap]
rs11167956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11743368	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12523317	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13165556	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13183391	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1383167	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1383168	0.83[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1480154	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs17105791	0.84[JPT][hapmap]
rs1842343	0.90[ASN][1000 genomes]
rs2054528	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2400234	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2400236	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2400241	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs61088380	0.86[ASN][1000 genomes]
rs62377581	0.89[ASN][1000 genomes]
rs62377606	0.81[EUR][1000 genomes]
rs6880660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6880992	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	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs922585	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9325031	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9325032	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs997979	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	chr5:146418800-146424200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:146419000-146422200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:146419000-146422400	Weak transcription	Brain Angular Gyrus	brain
4	chr5:146419200-146421400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:146419200-146422200	Weak transcription	Brain Anterior Caudate	brain
6	chr5:146419400-146422400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:146420400-146422200	Weak transcription	Brain Hippocampus Middle	brain
8	chr5:146421000-146421400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:146421000-146421400	Enhancers	Brain Substantia Nigra	brain
10	chr5:146421000-146422400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:146421000-146424400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:146421000-146425000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:146421000-146425000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:146421200-146421800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:146421200-146422200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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