Variant report

Variant	rs4925040
Chromosome Location	chr17:19588515-19588516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19587883..19589687-chr17:19605818..19607687,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1004490	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1004491	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1034897	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204407	0.85[ASN][1000 genomes]
rs12601634	0.81[AMR][1000 genomes]
rs12940877	0.84[AMR][1000 genomes]
rs2072332	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2120271	0.83[AMR][1000 genomes]
rs28672254	0.82[AMR][1000 genomes]
rs35364675	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3786038	0.88[ASN][1000 genomes]
rs4244600	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4621031	0.84[AMR][1000 genomes]
rs4646793	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4646800	0.85[ASN][1000 genomes]
rs4924791	0.82[AFR][1000 genomes]
rs4925026	0.81[AMR][1000 genomes]
rs4925037	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4925038	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4925041	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56262978	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61631401	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7502080	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs962801	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9902636	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9909886	0.80[EUR][1000 genomes];0.89[ASN][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
rs4925040	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 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	chr17:19580600-19589200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:19580800-19589600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:19582600-19594800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:19582600-19605600	Weak transcription	Fetal Kidney	kidney
9	chr17:19582800-19588600	Weak transcription	Esophagus	oesophagus
10	chr17:19582800-19589200	Weak transcription	Liver	Liver
11	chr17:19582800-19589600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:19582800-19589800	Weak transcription	HepG2	liver
13	chr17:19582800-19590000	Weak transcription	Gastric	stomach
14	chr17:19583000-19589600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:19583000-19590000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr17:19583000-19606200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr17:19583200-19591000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:19583200-19592000	Weak transcription	Fetal Intestine Small	intestine
19	chr17:19583400-19589200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr17:19583400-19606400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr17:19583400-19606800	Weak transcription	Ovary	ovary
22	chr17:19583600-19588600	Weak transcription	Brain Hippocampus Middle	brain
23	chr17:19585000-19605600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr17:19585000-19606600	Weak transcription	Pancreas	Pancrea
25	chr17:19585200-19589000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr17:19585200-19589800	Weak transcription	Fetal Stomach	stomach
27	chr17:19585200-19590000	Weak transcription	Fetal Muscle Leg	muscle
28	chr17:19585200-19593200	Weak transcription	A549	lung
29	chr17:19585200-19605600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr17:19585200-19606400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr17:19585200-19607000	Weak transcription	Aorta	Aorta
32	chr17:19585400-19591200	Weak transcription	Brain Angular Gyrus	brain
33	chr17:19586600-19588800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr17:19587200-19593000	Weak transcription	HSMMtube	muscle

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