Variant report

Variant	rs2731045
Chromosome Location	chr12:45471311-45471312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11182820	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182833	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182841	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12366891	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2544108	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2544109	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2544110	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2544113	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544114	0.92[EUR][1000 genomes]
rs2643154	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643155	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731033	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2731046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41427348	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[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
rs2731045	NELL2	cis	Adipose Subcutaneous	GTEx
rs2731045	NELL2	cis	Artery Tibial	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45469400-45472600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:45469800-45471400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:45469800-45471400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr12:45469800-45471800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr12:45470200-45471400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:45470400-45471600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr12:45470400-45471600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr12:45470600-45471400	Enhancers	H9 Cell Line	embryonic stem cell
9	chr12:45470600-45471400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr12:45470600-45471600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:45471000-45471400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:45471000-45471400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr12:45471000-45471400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr12:45471200-45472000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr12:45471200-45472200	Weak transcription	H1 Cell Line	embryonic stem cell

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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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