Variant report

Variant	rs6587201
Chromosome Location	chr17:19547493-19547494
allele	C/T
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:45)

rs_ID	r²[population]
rs11204408	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11656199	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11656773	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871420	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12150145	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12941194	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17684040	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1812051	0.84[AFR][1000 genomes]
rs2108971	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2120274	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165895	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2245639	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2386141	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2386142	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2386143	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2386145	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2440162	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2453586	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2453600	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2453601	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2453604	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2453608	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495827	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28537694	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3760489	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4273101	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4925036	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56109259	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62065943	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62065946	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587200	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7210433	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7216	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7405861	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7405862	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7502992	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069478	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8069576	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8074500	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074784	0.86[EUR][1000 genomes]
rs8079648	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs962800	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9889632	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903027	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	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
7	nsv543256	chr17:19515267-19547972	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6587201	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19538000-19549400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:19545000-19548800	Enhancers	Hela-S3	cervix
3	chr17:19545200-19548600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr17:19545400-19549600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr17:19545600-19550400	Enhancers	HepG2	liver
6	chr17:19545800-19550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr17:19546000-19549800	Weak transcription	HMEC	breast
8	chr17:19546200-19547600	Weak transcription	NHEK	skin
9	chr17:19546200-19550400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:19546400-19548000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:19546400-19548800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:19546400-19549400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:19546800-19548200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr17:19546800-19548800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr17:19547000-19549000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr17:19547000-19549000	Enhancers	A549	lung
17	chr17:19547000-19550200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:19547200-19549400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr17:19547400-19547800	Enhancers	Placenta	Placenta
20	chr17:19547400-19551800	Flanking Active TSS	Liver	Liver

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