Variant report

Variant	rs6549010
Chromosome Location	chr3:85089272-85089273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs28409084	1.00[AFR][1000 genomes]
rs28422781	1.00[AFR][1000 genomes]
rs28711631	1.00[AFR][1000 genomes]
rs6549008	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6799413	0.86[AFR][1000 genomes]
rs6807332	0.83[AFR][1000 genomes]
rs72917431	0.86[AFR][1000 genomes]
rs72917433	0.86[AFR][1000 genomes]
rs72917440	0.86[AFR][1000 genomes]
rs7630362	1.00[AFR][1000 genomes]
rs7636250	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7638859	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7645787	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7647977	1.00[AFR][1000 genomes]
rs7648767	1.00[YRI][hapmap]
rs9754888	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9754924	1.00[YRI][hapmap];1.00[AFR][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	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv492289	chr3:85066623-85319147	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2753915	chr3:85071410-85624810	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85068600-85090600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:85082600-85090000	Weak transcription	Fetal Brain Female	brain
3	chr3:85082600-85090400	Weak transcription	Fetal Brain Male	brain
4	chr3:85082600-85091600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:85083000-85090800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:85086800-85092000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:85088800-85089400	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr3:85088800-85089800	Enhancers	Brain Angular Gyrus	brain
9	chr3:85088800-85089800	Enhancers	Brain Anterior Caudate	brain
10	chr3:85089000-85089400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:85089000-85089600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:85089200-85089800	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr3:85089200-85090000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:85089200-85090000	Enhancers	Fetal Lung	lung

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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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