Variant report

Variant	rs10054914
Chromosome Location	chr5:112730216-112730217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10037845	0.87[YRI][hapmap]
rs10042401	1.00[ASW][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap]
rs10043512	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10050553	1.00[ASW][hapmap];0.88[MKK][hapmap]
rs10055294	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10061063	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10070884	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10077495	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10078931	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10478122	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11951897	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11960242	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12110055	0.85[YRI][hapmap]
rs13358281	0.87[YRI][hapmap]
rs7719254	0.82[YRI][hapmap]
rs7720243	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10054914	CHI3L2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112718800-112731400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:112720800-112731600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:112724400-112751200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:112729400-112730600	Enhancers	Fetal Stomach	stomach
5	chr5:112730000-112730600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:112730200-112738200	Weak transcription	HMEC	breast

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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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