Variant report

Variant	rs12480103
Chromosome Location	chr20:52338770-52338771
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2870276	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs34368454	0.84[ASN][1000 genomes]
rs6022697	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6022698	0.84[AMR][1000 genomes]
rs6091737	0.94[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.89[AMR][1000 genomes]
rs6097549	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6126927	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs62206459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055342	chr20:52126973-52352323	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	214 gene(s)	inside rSNPs	diseases
2	esv3412883	chr20:52176349-52393416	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
3	nsv834007	chr20:52213864-52404557	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	174 gene(s)	inside rSNPs	diseases
4	nsv912936	chr20:52250876-52344962	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv912937	chr20:52251863-52344962	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12480103	TSHZ2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52330400-52341600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:52331200-52340600	Weak transcription	Placenta	Placenta
3	chr20:52331200-52352600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr20:52332200-52340400	Weak transcription	HepG2	liver
5	chr20:52337400-52339000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr20:52337800-52339000	Enhancers	GM12878-XiMat	blood
7	chr20:52337800-52344600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr20:52338000-52341200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr20:52338200-52339400	Weak transcription	HUVEC	blood vessel
10	chr20:52338200-52341800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr20:52338600-52346000	Weak transcription	Primary B cells from cord blood	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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