Variant report

Variant	rs7969148
Chromosome Location	chr12:124614538-124614539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs427244	0.89[EUR][1000 genomes]
rs7302202	0.82[AMR][1000 genomes];0.97[EUR][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	nsv455734	chr12:124511908-124772515	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv560538	chr12:124511908-124772515	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv520633	chr12:124548394-124683205	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1799776	chr12:124594370-124614538	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Clubfoot	24667120	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7969148	KNTC1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124601000-124615200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:124608800-124615200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:124608800-124615200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:124609000-124615000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:124609000-124615000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:124609800-124615600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:124610400-124615000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:124610800-124615400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:124612800-124615400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:124613200-124615200	Enhancers	A549	lung
11	chr12:124613200-124617600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:124613800-124615200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:124613800-124615400	Enhancers	HepG2	liver
14	chr12:124613800-124617400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr12:124614000-124619600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:124614400-124614600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr12:124614400-124614600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr12:124614400-124615200	Enhancers	GM12878-XiMat	blood

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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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