Variant report

Variant	rs2386143
Chromosome Location	chr17:19589975-19589976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11204408	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11656199	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11656773	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11871420	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12150145	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12941194	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17684040	0.90[EUR][1000 genomes]
rs1812051	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2108970	0.80[AMR][1000 genomes]
rs2108971	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120274	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2159291	0.81[AMR][1000 genomes]
rs2165895	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2245639	0.90[EUR][1000 genomes]
rs2386141	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386142	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386145	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440162	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2453586	0.90[EUR][1000 genomes]
rs2453600	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2453601	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2453604	0.90[EUR][1000 genomes]
rs2453608	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28495827	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28537694	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760489	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4273101	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4925036	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109259	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62065943	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62065946	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6587200	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6587201	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7210433	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7215	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7216	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7405861	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7405862	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7502992	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8069478	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069576	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074500	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8074784	0.83[EUR][1000 genomes]
rs8079648	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs962800	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889632	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9903027	0.88[AMR][1000 genomes];0.93[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2386143	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19568600-19606800	Weak transcription	Psoas Muscle	Psoas
2	chr17:19569800-19591000	Weak transcription	Fetal Brain Male	brain
3	chr17:19575000-19590200	Weak transcription	Right Ventricle	heart
4	chr17:19576000-19596200	Weak transcription	Fetal Heart	heart
5	chr17:19582600-19594800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:19582600-19605600	Weak transcription	Fetal Kidney	kidney
7	chr17:19582800-19590000	Weak transcription	Gastric	stomach
8	chr17:19583000-19590000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr17:19583000-19606200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr17:19583200-19591000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr17:19583200-19592000	Weak transcription	Fetal Intestine Small	intestine
12	chr17:19583400-19606400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr17:19583400-19606800	Weak transcription	Ovary	ovary
14	chr17:19585000-19605600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr17:19585000-19606600	Weak transcription	Pancreas	Pancrea
16	chr17:19585200-19590000	Weak transcription	Fetal Muscle Leg	muscle
17	chr17:19585200-19593200	Weak transcription	A549	lung
18	chr17:19585200-19605600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr17:19585200-19606400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr17:19585200-19607000	Weak transcription	Aorta	Aorta
21	chr17:19585400-19591200	Weak transcription	Brain Angular Gyrus	brain
22	chr17:19587200-19593000	Weak transcription	HSMMtube	muscle
23	chr17:19588800-19591800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr17:19589000-19590400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr17:19589200-19590600	Enhancers	Liver	Liver
26	chr17:19589600-19590400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr17:19589800-19590200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:19589800-19590400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr17:19589800-19590400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:19589800-19590400	Enhancers	HepG2	liver

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