Variant report

Variant	rs6661124
Chromosome Location	chr1:86297442-86297443
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:10)

rs_ID	r²[population]
rs10158651	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10159046	0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12239978	1.00[ASW][hapmap];0.87[LWK][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2389988	1.00[MEX][hapmap]
rs6676346	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952531	0.83[AFR][1000 genomes]
rs7516136	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7530774	1.00[MEX][hapmap]
rs7535390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs980054	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv546721	chr1:86226352-86392577	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv999743	chr1:86241246-86364846	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1011293	chr1:86270649-86416972	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
8	esv15952	chr1:86296641-86297551	ZNF genes & repeats Weak transcription Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases
9	nsv546723	chr1:86296663-86297495	ZNF genes & repeats Enhancers Strong transcription Weak transcription	n/a	n/a	inside rSNPs	diseases
10	nsv546724	chr1:86296714-86297495	Weak transcription ZNF genes & repeats Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases
11	nsv546725	chr1:86296817-86297495	ZNF genes & repeats Strong transcription Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86296200-86297800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:86296400-86297600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
3	chr1:86296400-86297600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr1:86296400-86297600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:86297000-86315400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:86297400-86297600	ZNF genes & repeats	Fetal Lung	lung
7	chr1:86297400-86303600	Weak transcription	GM12878-XiMat	blood

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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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