Variant report

Variant	rs2544109
Chromosome Location	chr12:45483229-45483230
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11182820	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11182833	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11182841	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12366891	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2408141	0.88[EUR][1000 genomes]
rs2544108	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2544110	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544113	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2544114	0.83[EUR][1000 genomes]
rs2643154	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2643155	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2731033	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2731045	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2731046	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41427348	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3351644	chr12:45345597-45529449	Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2544109	NELL2	cis	Artery Tibial	GTEx
rs2544109	NELL2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45481600-45484000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:45482400-45484000	Enhancers	Adipose Nuclei	Adipose
3	chr12:45482600-45483800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:45482600-45484000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:45482600-45484200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr12:45482800-45484200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:45483000-45483600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:45483000-45484000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr12:45483000-45484200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:45483000-45484200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr12:45483000-45484800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr12:45483200-45483400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr12:45483200-45483800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:45483200-45483800	Enhancers	Brain Germinal Matrix	brain
15	chr12:45483200-45484000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr12:45483200-45484200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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