Variant report

Variant	rs4454130
Chromosome Location	chr6:38460901-38460902
allele	C/T
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:23)

rs_ID	r²[population]
rs11964058	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12200371	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12524209	0.88[ASN][1000 genomes]
rs12526608	0.82[ASN][1000 genomes]
rs12528414	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12528646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12528840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16890682	0.92[CHB][hapmap]
rs16890715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16890751	1.00[JPT][hapmap]
rs28587676	0.82[ASN][1000 genomes]
rs28889620	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35978718	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4236059	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs4316001	1.00[JPT][hapmap]
rs58163486	0.88[ASN][1000 genomes]
rs61088409	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6912811	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6914430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6941817	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7764900	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9470889	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs9470890	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38449800-38461600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:38450000-38461000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:38450600-38469800	Weak transcription	HSMMtube	muscle
5	chr6:38450800-38461600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:38451000-38461000	Weak transcription	Fetal Brain Male	brain
7	chr6:38451600-38471000	Weak transcription	Psoas Muscle	Psoas
8	chr6:38452400-38496600	Weak transcription	Primary B cells from cord blood	blood
9	chr6:38454000-38461000	Weak transcription	GM12878-XiMat	blood
10	chr6:38454400-38486400	Weak transcription	Primary T cells from cord blood	blood
11	chr6:38455600-38461200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:38457800-38461400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:38460000-38461200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:38460000-38461200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:38460000-38464600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:38460200-38461200	Weak transcription	Brain Substantia Nigra	brain
17	chr6:38460200-38461400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:38460200-38462800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:38460800-38461800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:38460800-38473000	Enhancers	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links