Variant report

Variant	rs28434705
Chromosome Location	chr3:53798335-53798336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53797911..53799633-chr3:53804369..53806585,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11719163	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918583	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28365115	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3774567	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3774570	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774577	0.83[EUR][1000 genomes]
rs3774580	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821860	0.87[EUR][1000 genomes]
rs3821866	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3846215	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276449	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56384446	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6776947	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797014	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs714786	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311514	0.97[AMR][1000 genomes];0.93[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53768600-53801000	Strong transcription	Fetal Lung	lung
2	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
3	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine
4	chr3:53778600-53806400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:53779000-53806400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:53780400-53807000	Weak transcription	Fetal Brain Female	brain
7	chr3:53781800-53807400	Weak transcription	Brain Anterior Caudate	brain
8	chr3:53785000-53811200	Weak transcription	Spleen	Spleen
9	chr3:53785800-53806600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:53786000-53808200	Weak transcription	Liver	Liver
11	chr3:53788800-53798400	Weak transcription	Lung	lung
12	chr3:53788800-53807000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:53789800-53814600	Weak transcription	Brain Substantia Nigra	brain
14	chr3:53796000-53801800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:53796400-53806800	Weak transcription	Brain Angular Gyrus	brain
16	chr3:53796600-53799000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:53796600-53807000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:53796800-53808000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:53797400-53798400	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr3:53798000-53798400	Weak transcription	Pancreas	Pancrea
21	chr3:53798000-53807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:53798200-53798800	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links