Variant report

Variant	rs55997059
Chromosome Location	chr3:49858661-49858662
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11130217	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709734	0.94[EUR][1000 genomes]
rs11720705	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12715437	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1491985	0.94[EUR][1000 genomes]
rs1799844	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1996663	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1996664	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28535523	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3020779	0.81[EUR][1000 genomes]
rs35129566	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58339610	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59357103	0.96[EUR][1000 genomes]
rs59684465	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61557789	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62260663	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62260720	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62260723	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62262722	0.95[EUR][1000 genomes]
rs62262730	0.96[EUR][1000 genomes]
rs6790568	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804970	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809879	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7613603	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7620848	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621797	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7628207	0.89[EUR][1000 genomes]
rs7637711	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649428	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9829155	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9835157	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9836756	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9851651	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9870755	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9870858	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv967270	chr3:49845381-49870409	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs55997059	AMT	cis	lung	GTEx
rs55997059	NICN1-AS1	cis	Thyroid	GTEx
rs55997059	NICN1	cis	Thyroid	GTEx
rs55997059	AMT	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49843400-49866400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:49851800-49866000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:49852000-49864800	Weak transcription	Fetal Thymus	thymus
4	chr3:49852000-49865200	Weak transcription	Fetal Intestine Small	intestine
5	chr3:49852000-49866200	Weak transcription	Thymus	Thymus
6	chr3:49852400-49866000	Weak transcription	GM12878-XiMat	blood
7	chr3:49856200-49866200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:49857200-49865000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:49857600-49865600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49857800-49865000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:49858400-49865800	Weak transcription	Esophagus	oesophagus

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