Variant report

Variant	rs12525079
Chromosome Location	chr6:141793159-141793160
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10499226	0.89[EUR][1000 genomes]
rs11155185	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11155189	0.90[EUR][1000 genomes]
rs4386830	0.85[EUR][1000 genomes]
rs4472370	0.85[EUR][1000 genomes]
rs55959773	0.89[EUR][1000 genomes]
rs62430845	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6905051	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9373311	0.86[EUR][1000 genomes]
rs9376630	0.88[EUR][1000 genomes]
rs9389931	0.87[EUR][1000 genomes]
rs9399371	0.90[EUR][1000 genomes]
rs9399372	0.90[EUR][1000 genomes]
rs9403308	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9403315	0.90[EUR][1000 genomes]
rs9403317	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9403320	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019459	chr6:141051249-141862727	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv538453	chr6:141051249-141862727	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv532070	chr6:141057326-141865359	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1025922	chr6:141090901-141865360	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv538454	chr6:141090901-141865360	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1029550	chr6:141372610-142029669	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv886727	chr6:141610933-141793547	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1015835	chr6:141713451-142233317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv538455	chr6:141713451-142233317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	esv2755719	chr6:141721907-142123546	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr6:141786600-141796400	Weak transcription	HSMM	muscle
2	chr6:141787800-141795800	Weak transcription	Psoas Muscle	Psoas
3	chr6:141791400-141793200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
4	chr6:141792400-141794000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr6:141792400-141794200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr6:141792800-141793200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:141792800-141793200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:141792800-141793200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:141792800-141794000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr6:141792800-141794200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr6:141792800-141794600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:141793000-141793200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:141793000-141793800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr6:141793000-141794200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:141793000-141794400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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