Variant report

Variant	rs16858233
Chromosome Location	chr1:166923584-166923585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10465566	0.81[EUR][1000 genomes]
rs10489574	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12757660	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17331190	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs33958744	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34055645	0.85[EUR][1000 genomes]
rs34925982	0.80[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs36110323	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36119409	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73026741	0.93[AFR][1000 genomes]
rs73026798	0.81[AFR][1000 genomes]
rs73026802	0.85[AFR][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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16858233	MAEL	cis	brain	BrainEAC
rs16858233	APOA2	cis	cerebellum	SCAN
rs16858233	MAEL	cis	parietal	SCAN
rs16858233	ANKRD36BP1	cis	parietal	SCAN
rs16858233	UCK2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166915400-166923800	Weak transcription	Dnd41	blood
2	chr1:166919400-166936400	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:166919600-166929400	Weak transcription	Thymus	Thymus
4	chr1:166920000-166928200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:166921400-166927200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:166921400-166927600	Weak transcription	Brain Anterior Caudate	brain
7	chr1:166921600-166935800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:166921800-166924000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:166921800-166924000	Weak transcription	Brain Angular Gyrus	brain
10	chr1:166922000-166933800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:166922200-166927800	Weak transcription	HSMMtube	muscle
12	chr1:166922400-166927600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:166922600-166925200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:166922800-166925000	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:166922800-166930200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:166923000-166925600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:166923000-166928600	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:166923200-166927000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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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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