Variant report

Variant	rs9839560
Chromosome Location	chr3:51322919-51322920
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13326334	0.86[AFR][1000 genomes]
rs13326339	0.86[AFR][1000 genomes]
rs13433759	0.87[AFR][1000 genomes]
rs58562986	0.87[AFR][1000 genomes]
rs9311468	0.86[AFR][1000 genomes]
rs9810160	0.86[AFR][1000 genomes]
rs9826823	0.87[AFR][1000 genomes]
rs9826836	0.86[AFR][1000 genomes]
rs9841448	0.87[AFR][1000 genomes]
rs9851972	0.86[AFR][1000 genomes]
rs9854165	0.86[AFR][1000 genomes]
rs9856721	0.87[AFR][1000 genomes]
rs9860032	0.87[AFR][1000 genomes]
rs9862968	0.87[AFR][1000 genomes]
rs9871213	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51308200-51323000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:51313000-51323800	Weak transcription	Fetal Brain Male	brain
3	chr3:51315400-51350000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:51318200-51328600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:51318600-51324400	Weak transcription	Brain Substantia Nigra	brain
6	chr3:51319600-51324000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:51319600-51324200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:51319800-51323800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:51320000-51324200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:51320800-51323000	Strong transcription	Brain Germinal Matrix	brain
11	chr3:51321000-51324400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:51321000-51324600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:51321400-51323800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:51322600-51324600	Weak transcription	Brain Anterior Caudate	brain
15	chr3:51322600-51329000	Weak transcription	Brain Angular Gyrus	brain
16	chr3:51322800-51323800	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:51322800-51327800	Weak transcription	Brain Cingulate Gyrus	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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