Variant report

Variant	rs2453586
Chromosome Location	chr17:19494756-19494757
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11204408	0.81[EUR][1000 genomes]
rs11656199	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11656773	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11871420	0.90[EUR][1000 genomes]
rs12150145	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12941194	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17684040	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108971	0.89[CEU][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs2120274	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2165895	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245639	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386141	0.81[GIH][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap]
rs2386142	0.83[YRI][hapmap]
rs2386143	0.90[EUR][1000 genomes]
rs2386145	0.89[CEU][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes]
rs2440162	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453600	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453601	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453604	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453608	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28495827	0.89[EUR][1000 genomes]
rs3760489	0.87[EUR][1000 genomes]
rs4273101	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4925036	0.88[CEU][hapmap];0.88[YRI][hapmap];0.89[EUR][1000 genomes]
rs56109259	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62065943	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62065946	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587200	0.87[EUR][1000 genomes]
rs6587201	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7210433	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7215	0.89[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs7216	0.89[CEU][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs7405861	0.85[EUR][1000 genomes]
rs7405862	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7502992	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8069478	0.85[EUR][1000 genomes]
rs8069576	0.89[CEU][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs8074500	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8074784	0.82[EUR][1000 genomes]
rs8079648	0.92[EUR][1000 genomes]
rs962800	0.89[CEU][hapmap];0.92[GIH][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs9889632	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9903027	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1056125	chr17:19484803-19536116	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1059195	chr17:19484803-19547972	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv2757654	chr17:19485735-19563766	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	esv2758679	chr17:19485735-19563766	Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv437815	chr17:19488851-19545834	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv437816	chr17:19488851-19545834	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1058163	chr17:19492744-19536116	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv521483	chr17:19494178-19494756	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
12	nsv528606	chr17:19494178-19495478	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
13	nsv817754	chr17:19494178-19495478	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
14	nsv817755	chr17:19494178-19517768	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases
15	esv3693233	chr17:19494178-19537470	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv9505	chr17:19494186-19495742	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
17	nsv574575	chr17:19494756-19534434	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2453586	ALDH3A2	cis	cerebellum	SCAN
rs2453586	MAP2K3	cis	cerebellum	SCAN
rs2453586	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs2453586	ALDH3A2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19493200-19494800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr17:19493200-19499200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr17:19493400-19499200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:19493600-19494800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr17:19494200-19495000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr17:19494200-19495200	Enhancers	HepG2	liver
7	chr17:19494400-19495000	Enhancers	Cortex derived primary cultured neurospheres	brain

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