Variant report

Variant	rs12869943
Chromosome Location	chr13:38356247-38356248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10507458	1.00[JPT][hapmap]
rs12875527	1.00[JPT][hapmap]
rs17056501	0.86[JPT][hapmap]
rs17056503	0.86[JPT][hapmap]
rs17263147	1.00[JPT][hapmap]
rs17265071	1.00[JPT][hapmap]
rs2184125	1.00[JPT][hapmap]
rs3829362	1.00[JPT][hapmap]
rs4399429	1.00[JPT][hapmap]
rs928494	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753974	chr13:38341331-38363450	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv33246	chr13:38353893-38357951	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12869943	TRPC4	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38352600-38357200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr13:38354200-38357200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr13:38354600-38356600	Enhancers	Rectal Smooth Muscle	rectum
4	chr13:38354600-38356800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr13:38354800-38356400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:38355600-38356600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:38355600-38357000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:38355800-38356400	Enhancers	Osteobl	bone
9	chr13:38355800-38356800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:38355800-38359600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:38356200-38363400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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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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