Variant report

Variant	rs9864401
Chromosome Location	chr3:180124294-180124295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1532485	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs17764356	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62290974	0.84[EUR][1000 genomes]
rs6770664	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs7626274	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9290705	0.85[AMR][1000 genomes]
rs9832227	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9847201	0.85[AMR][1000 genomes]
rs9864959	0.88[AMR][1000 genomes]
rs9865590	1.00[YRI][hapmap]
rs9866580	0.88[AMR][1000 genomes]
rs9872076	0.88[AMR][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	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180120800-180126400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:180121200-180126200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:180121600-180126400	Weak transcription	NHEK	skin
4	chr3:180122200-180126000	Weak transcription	HMEC	breast
5	chr3:180122400-180126200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:180124200-180124600	Active TSS	Hela-S3	cervix

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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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