Variant report

Variant	rs2389553
Chromosome Location	chr7:15888046-15888047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10486775	1.00[MEX][hapmap]
rs17169101	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17169105	1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs17169107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73680224	1.00[EUR][1000 genomes]
rs7797334	0.94[EUR][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	nsv932168	chr7:15573437-15895294	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv523199	chr7:15582208-16042596	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2389553	IL17RB	trans	lymphoblastoid	seeQTL
rs2389553	SLC46A3	trans	lymphoblastoid	seeQTL
rs2389553	TXNIP	trans	lymphoblastoid	seeQTL
rs2389553	ITGAX	trans	lymphoblastoid	seeQTL
rs2389553	TNFRSF21	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:15879800-15890800	Weak transcription	Fetal Muscle Leg	muscle
2	chr7:15885000-15890400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:15886200-15888200	Weak transcription	Fetal Lung	lung
4	chr7:15887400-15888600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:15887600-15888600	Enhancers	Osteobl	bone
6	chr7:15887600-15889400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:15888000-15888400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:15888000-15888600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:15888000-15888600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:15888000-15888600	Enhancers	Adipose Nuclei	Adipose
11	chr7:15888000-15888800	Enhancers	Primary hematopoietic stem cells	blood
12	chr7:15888000-15888800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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