Variant report

Variant	rs4938854
Chromosome Location	chr11:56997434-56997435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11228958	0.99[ASN][1000 genomes]
rs11820215	0.86[CEU][hapmap];0.94[GIH][hapmap]
rs2077190	0.86[CEU][hapmap];0.94[GIH][hapmap]
rs35783847	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4939117	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4939118	0.86[ASN][1000 genomes]
rs567766	0.86[CEU][hapmap];0.94[GIH][hapmap]
rs609763	0.86[CEU][hapmap];0.94[GIH][hapmap]
rs622932	0.86[CEU][hapmap]
rs948851	0.86[CEU][hapmap];0.94[GIH][hapmap]

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	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv482317	chr11:56857026-57028631	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4938854	TIMM10	cis	parietal	SCAN
rs4938854	OR4C15	cis	parietal	SCAN
rs4938854	OR5T3	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56987600-57000800	Weak transcription	Spleen	Spleen
2	chr11:56989600-56997800	Weak transcription	Adipose Nuclei	Adipose
3	chr11:56992600-56997800	Weak transcription	HSMMtube	muscle
4	chr11:56992600-56998600	Weak transcription	Brain Anterior Caudate	brain
5	chr11:56992800-56997600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:56992800-56998400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:56994000-56997600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:56996000-56998000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:56996200-56998400	Weak transcription	Right Ventricle	heart
10	chr11:56996600-56998600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr11:56996800-56998400	Weak transcription	Left Ventricle	heart
12	chr11:56997200-56998400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:56997400-56997600	Enhancers	HSMM	muscle
14	chr11:56997400-56998000	Enhancers	Brain Cingulate Gyrus	brain
15	chr11:56997400-56998400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:56997400-56998800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:56997400-56999000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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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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