Variant report

Variant	rs10223990
Chromosome Location	chr7:18979516-18979517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10250414	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1034805	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.96[ASN][1000 genomes]
rs10486329	0.81[CHB][hapmap]
rs10486330	0.81[CHB][hapmap]
rs11505418	0.81[CHB][hapmap]
rs2051923	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498112	chr7:18677922-18991946	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv887813	chr7:18720135-18995552	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv531020	chr7:18971153-19261019	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10223990	TMPRSS3	trans	lymphoblastoid	seeQTL
rs10223990	LRIG1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:18976400-18980400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr7:18977400-18980600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr7:18978200-18980000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
4	chr7:18978400-18980200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr7:18978600-18979600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:18979200-18979800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:18979200-18980000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:18979200-18980000	Enhancers	HUVEC	blood vessel
9	chr7:18979200-18981400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr7:18979200-18982000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr7:18979400-18979800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:18979400-18980000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:18979400-18980400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr7:18979400-18981200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:18979400-18981600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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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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