Variant report

Variant	rs11119543
Chromosome Location	chr1:210762289-210762290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11119544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119550	0.82[ASN][1000 genomes]
rs12024921	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12034711	0.94[EUR][1000 genomes]
rs12069347	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12745924	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4077408	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951722	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs6691952	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][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	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv873149	chr1:210749312-210793972	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11119543	IKBKE	cis	parietal	SCAN
rs11119543	NUCKS1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210756200-210771800	Weak transcription	Left Ventricle	heart
2	chr1:210758600-210763000	Weak transcription	A549	lung
3	chr1:210760400-210763200	Weak transcription	Brain Anterior Caudate	brain
4	chr1:210760400-210763200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:210760600-210763200	Weak transcription	Brain Angular Gyrus	brain
6	chr1:210760800-210763000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:210761000-210762400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:210761000-210763200	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:210761000-210763200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:210761400-210762400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:210761400-210762800	Weak transcription	NH-A	brain
12	chr1:210761400-210771600	Weak transcription	Gastric	stomach
13	chr1:210761600-210762400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:210761600-210762800	Weak transcription	Ovary	ovary
15	chr1:210761600-210763000	Weak transcription	HSMMtube	muscle
16	chr1:210761600-210770400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:210762000-210763200	Enhancers	Osteobl	bone
18	chr1:210762200-210762400	Enhancers	HSMM	muscle

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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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