Variant report

Variant	rs12004028
Chromosome Location	chr9:108182999-108183000
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10115811	0.83[AMR][1000 genomes]
rs10115838	0.83[AMR][1000 genomes]
rs10119410	0.83[AMR][1000 genomes]
rs10119483	0.83[AMR][1000 genomes]
rs10121304	0.83[AMR][1000 genomes]
rs10123783	0.83[AMR][1000 genomes]
rs10125150	0.83[AMR][1000 genomes]
rs10125368	0.83[AMR][1000 genomes]
rs10441742	0.83[AMR][1000 genomes]
rs10441743	0.83[AMR][1000 genomes]
rs10441771	0.83[AMR][1000 genomes]
rs10441772	0.83[AMR][1000 genomes]
rs10441773	0.83[AMR][1000 genomes]
rs10441774	0.83[AMR][1000 genomes]
rs12336341	0.83[AMR][1000 genomes]
rs12337845	0.83[AMR][1000 genomes]
rs12338480	0.83[AMR][1000 genomes]
rs12340242	0.83[AMR][1000 genomes]
rs12345255	0.83[AMR][1000 genomes]
rs12346497	0.83[AMR][1000 genomes]
rs12348967	0.83[AMR][1000 genomes]
rs12349041	0.83[AMR][1000 genomes]
rs12349068	0.83[AMR][1000 genomes]
rs28456113	0.83[AMR][1000 genomes]
rs28461171	0.83[AMR][1000 genomes]
rs28541347	0.83[AMR][1000 genomes]
rs28613030	1.00[AMR][1000 genomes]
rs56965223	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57430142	0.83[AMR][1000 genomes]
rs57497195	1.00[AMR][1000 genomes]
rs7028140	0.83[AMR][1000 genomes]
rs9299388	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 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	chr9:108176200-108188200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:108177600-108186400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:108177800-108194200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:108177800-108194200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:108179200-108183200	Enhancers	Fetal Brain Male	brain
6	chr9:108179600-108184200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr9:108180600-108183400	Enhancers	Fetal Brain Female	brain
8	chr9:108180600-108184400	Enhancers	Brain Hippocampus Middle	brain
9	chr9:108181000-108183000	Enhancers	Brain Anterior Caudate	brain
10	chr9:108181800-108183000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:108181800-108184800	Enhancers	HepG2	liver
12	chr9:108182000-108183000	Flanking Active TSS	Liver	Liver
13	chr9:108182200-108184000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:108182600-108193800	Weak transcription	Brain Angular Gyrus	brain
15	chr9:108182600-108193800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:108182800-108184000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr9:108182800-108193600	Weak transcription	Brain Substantia Nigra	brain
18	chr9:108182800-108193800	Weak transcription	Brain Inferior Temporal Lobe	brain

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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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