Variant report

Variant	rs12671280
Chromosome Location	chr7:136979249-136979250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10247519	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10251438	0.85[JPT][hapmap]
rs12668246	0.85[JPT][hapmap]
rs13245564	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17169033	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17169050	0.82[CHB][hapmap]
rs2242045	0.85[JPT][hapmap]
rs6977749	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6977819	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029192	chr7:136433278-137147566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831149	chr7:136831665-137006468	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv889238	chr7:136915059-136989606	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv889239	chr7:136923730-136994013	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv889240	chr7:136972027-137038092	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv889241	chr7:136976713-137038092	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12671280	CNOT4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:136938200-136980600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:136961400-136980600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:136968600-136989600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:136972200-136979400	Weak transcription	Brain Angular Gyrus	brain
5	chr7:136972200-136990400	Weak transcription	Fetal Stomach	stomach
6	chr7:136974600-136982600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:136974600-136983600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:136975200-136982600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:136975200-136991000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:136976600-136991000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:136977200-136980000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:136977200-136980600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:136978200-136983400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:136978400-136979400	Enhancers	Brain Substantia Nigra	brain
15	chr7:136978800-136981200	Enhancers	Brain Hippocampus Middle	brain
16	chr7:136979000-136979400	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr7:136979000-136981000	Enhancers	Brain Cingulate Gyrus	brain
18	chr7:136979200-136979600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:136979200-136989800	Enhancers	Cortex derived primary cultured neurospheres	brain

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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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