Variant report

Variant	rs2072741
Chromosome Location	chr1:166929664-166929665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1053407	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11582566	0.81[CEU][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2013526	0.85[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs2014854	0.85[CEU][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2075981	0.81[CEU][hapmap];0.86[LWK][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs2075982	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312238	0.85[CEU][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2837	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs393025	0.92[CEU][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs402031	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs453395	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4657614	0.81[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs6427046	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6688277	0.81[EUR][1000 genomes]
rs6690192	0.89[TSI][hapmap]
rs7552562	0.85[CEU][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs926266	0.80[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[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	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2072741	GPR161	cis	cerebellum	SCAN
rs2072741	TBX19	cis	cerebellum	SCAN
rs2072741	MAEL	cis	lymphoblastoid	seeQTL
rs2072741	MAEL	cis	Nerve Tibial	GTEx
rs2072741	ANKRD36BP1	cis	parietal	SCAN
rs2072741	MAEL	cis	Thyroid	GTEx
rs2072741	MAEL	cis	Esophagus Muscularis	GTEx
rs2072741	UAP1	cis	cerebellum	SCAN
rs2072741	MAEL	cis	parietal	SCAN
rs2072741	DUSP12	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166919400-166936400	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:166921600-166935800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:166922000-166933800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:166922800-166930200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:166926400-166932400	Weak transcription	Dnd41	blood
6	chr1:166926800-166934000	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:166927200-166934000	Weak transcription	GM12878-XiMat	blood
8	chr1:166927200-166937200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:166927400-166941600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:166927600-166940200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:166927800-166940000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:166928600-166932400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:166929400-166930200	Enhancers	Fetal Kidney	kidney

Quick Search:

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

what's new

Quick links