Variant report

Variant	rs2386141
Chromosome Location	chr17:19595936-19595937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12150145	0.81[AMR][1000 genomes]
rs1812051	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2108970	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2108971	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2386143	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386145	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28537694	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925036	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62065946	0.81[AMR][1000 genomes]
rs6587201	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7210433	0.81[AMR][1000 genomes]
rs7216	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069478	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8069576	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074500	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8081130	1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs962800	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889632	0.83[AFR][1000 genomes];0.83[AMR][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	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1062485	chr17:19558644-19608008	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2386141	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs2386141	ALDH3A2	cis	cerebellum	SCAN
rs2386141	ALDH3A2	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19568600-19606800	Weak transcription	Psoas Muscle	Psoas
2	chr17:19576000-19596200	Weak transcription	Fetal Heart	heart
3	chr17:19582600-19605600	Weak transcription	Fetal Kidney	kidney
4	chr17:19583000-19606200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr17:19583400-19606400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr17:19583400-19606800	Weak transcription	Ovary	ovary
7	chr17:19585000-19605600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr17:19585000-19606600	Weak transcription	Pancreas	Pancrea
9	chr17:19585200-19605600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr17:19585200-19606400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr17:19585200-19607000	Weak transcription	Aorta	Aorta
12	chr17:19590400-19600000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:19590600-19607400	Weak transcription	Liver	Liver
14	chr17:19592400-19606200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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