Variant report

Variant	rs2213162
Chromosome Location	chr12:48390722-48390723
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]
rs12228854	0.95[CHB][hapmap]
rs12308909	0.86[ASN][1000 genomes]
rs1635533	0.95[EUR][1000 genomes]
rs1793953	0.87[CEU][hapmap];0.94[EUR][1000 genomes]
rs1793954	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs2023939	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2213163	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2226946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248990	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276453	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3737548	0.97[ASN][1000 genomes]
rs3809322	0.95[CHB][hapmap]
rs56037230	0.97[ASN][1000 genomes]
rs56959315	0.97[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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2213162	H1FNT	cis	Muscle Skeletal	GTEx
rs2213162	ZNF641	cis	Muscle Skeletal	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:48382800-48394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:48383800-48393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48383800-48394400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48385200-48391600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:48386800-48392800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48387000-48391600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:48388000-48391400	Enhancers	Fetal Brain Male	brain
9	chr12:48389200-48391000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr12:48389400-48391000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:48389800-48391200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:48389800-48391800	Enhancers	Liver	Liver
13	chr12:48390000-48395000	Weak transcription	Right Atrium	heart
14	chr12:48390200-48391000	Weak transcription	Fetal Intestine Small	intestine
15	chr12:48390200-48391200	Weak transcription	Placenta	Placenta
16	chr12:48390200-48391800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:48390400-48394600	Weak transcription	Left Ventricle	heart
18	chr12:48390400-48394600	Weak transcription	Right Ventricle	heart
19	chr12:48390600-48391800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	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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