Variant report

Variant	rs28889620
Chromosome Location	chr6:38453789-38453790
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38447684..38449733-chr6:38451099..38453869,2	K562	blood:

Variant related genes	Relation type
ENSG00000226533	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11964058	0.90[ASN][1000 genomes]
rs12200371	0.81[AFR][1000 genomes]
rs12524209	0.90[ASN][1000 genomes]
rs12526608	0.84[ASN][1000 genomes]
rs12528414	0.84[ASN][1000 genomes]
rs12528646	0.90[ASN][1000 genomes]
rs12528840	0.90[ASN][1000 genomes]
rs16890715	0.90[ASN][1000 genomes]
rs28587676	0.84[ASN][1000 genomes]
rs35978718	0.98[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4236059	0.83[EUR][1000 genomes]
rs4400204	0.82[ASN][1000 genomes]
rs4454130	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58163486	0.90[ASN][1000 genomes]
rs61088409	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6912811	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6914430	0.85[ASN][1000 genomes]
rs6941817	0.89[ASN][1000 genomes]
rs7764900	0.85[ASN][1000 genomes]
rs9470890	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38437000-38455400	Weak transcription	Gastric	stomach
2	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:38446600-38455400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:38449800-38461600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:38450000-38461000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:38450600-38469800	Weak transcription	HSMMtube	muscle
7	chr6:38450800-38455200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:38450800-38458000	Weak transcription	Fetal Lung	lung
9	chr6:38450800-38461600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:38451000-38461000	Weak transcription	Fetal Brain Male	brain
11	chr6:38451600-38471000	Weak transcription	Psoas Muscle	Psoas
12	chr6:38452000-38454000	Enhancers	GM12878-XiMat	blood
13	chr6:38452400-38496600	Weak transcription	Primary B cells from cord blood	blood
14	chr6:38452800-38455000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:38453200-38454000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:38453400-38454400	Strong transcription	Primary T cells from cord blood	blood
17	chr6:38453400-38457800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:38453400-38458400	Weak transcription	Primary B cells from peripheral blood	blood

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