Variant report

Variant	rs2010728
Chromosome Location	chr17:19623533-19623534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB7A	chr17:19623522-19624751	ECC-1	luminal epithelium:	n/a	n/a
2	ESR1	chr17:19623121-19623770	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
3	NR3C1	chr17:19623246-19623764	A549	lung:	n/a	n/a
4	YY1	chr17:19623072-19624720	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr17:19623035-19624610	ECC-1	luminal epithelium:	n/a	chr17:19624504-19624514
6	ESR1	chr17:19622946-19624505	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
7	ESR1	chr17:19623101-19624392	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
8	NR3C1	chr17:19623202-19623649	ECC-1	luminal epithelium:	n/a	n/a
9	EP300	chr17:19622981-19624687	ECC-1	luminal epithelium:	n/a	chr17:19623022-19623029
10	TEAD4	chr17:19623005-19624707	ECC-1	luminal epithelium:	n/a	n/a
11	TEAD4	chr17:19622607-19624645	ECC-1	luminal epithelium:	n/a	n/a
12	NR3C1	chr17:19623266-19623620	ECC-1	luminal epithelium:	n/a	n/a
13	ZBTB7A	chr17:19622788-19624774	ECC-1	luminal epithelium:	n/a	chr17:19622910-19622918 chr17:19622983-19622997 chr17:19622984-19622998 chr17:19622911-19622919
14	NFIC	chr17:19622613-19624764	ECC-1	luminal epithelium:	n/a	chr17:19624229-19624246 chr17:19624230-19624246
15	TCF12	chr17:19622858-19624837	ECC-1	luminal epithelium:	n/a	chr17:19624809-19624816 chr17:19624811-19624818
16	YY1	chr17:19623152-19624566	ECC-1	luminal epithelium:	n/a	n/a
17	MAX	chr17:19623016-19624864	ECC-1	luminal epithelium:	n/a	chr17:19624504-19624514
18	ESR1	chr17:19622971-19624446	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
19	EP300	chr17:19622762-19624918	ECC-1	luminal epithelium:	n/a	chr17:19623022-19623029
20	FOXM1	chr17:19623029-19624701	ECC-1	luminal epithelium:	n/a	n/a
21	NFIC	chr17:19622501-19624942	ECC-1	luminal epithelium:	n/a	chr17:19624229-19624246 chr17:19624230-19624246
22	ESR1	chr17:19623135-19623682	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
23	FOXM1	chr17:19622946-19624798	ECC-1	luminal epithelium:	n/a	n/a
24	TFAP2C	chr17:19622515-19624604	Hela-S3	cervix:	n/a	n/a
25	TCF12	chr17:19623013-19624857	ECC-1	luminal epithelium:	n/a	chr17:19624809-19624816 chr17:19624811-19624818
26	ESR1	chr17:19622953-19624569	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
27	RAD21	chr17:19623104-19624565	ECC-1	luminal epithelium:	n/a	chr17:19624501-19624511 chr17:19624516-19624525 chr17:19623819-19623838

No.	Distal block	Cell Line	Cell type
1	chr17:19623453..19625417-chr17:19651526..19653973,2	MCF-7	breast:
2	chr17:19616686..19619985-chr17:19620299..19623719,4	MCF-7	breast:
3	chr17:19550345..19551966-chr17:19622078..19623602,2	MCF-7	breast:
4	chr17:19617555..19619828-chr17:19622180..19625084,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALDH3A2-1	chr17:19622372-19625741	ENSG00000262681.2
2	lnc-ALDH3A1-1	chr17:19621424-19623686	NONHSAT146521

Variant related genes	Relation type
SLC47A2	TF binding region
ENSG00000072210	Chromatin interaction
ENSG00000108602	Chromatin interaction
ENSG00000180638	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1006554	0.85[EUR][1000 genomes]
rs11204411	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11204412	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11204413	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11204414	0.81[EUR][1000 genomes]
rs12945122	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12948735	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2108967	0.82[EUR][1000 genomes]
rs4924793	0.85[EUR][1000 genomes]
rs7209418	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7214841	0.90[EUR][1000 genomes]
rs7222877	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8077368	0.84[EUR][1000 genomes]
rs9898022	0.81[AMR][1000 genomes]
rs9910370	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	esv1807724	chr17:19597423-19656009	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh 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	21 gene(s)	inside rSNPs	diseases
7	esv1793043	chr17:19604821-19670329	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv526290	chr17:19613357-19651482	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv457704	chr17:19620477-19663747	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv470582	chr17:19620477-19663747	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv574580	chr17:19620477-19663747	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2010728	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19607600-19627400	Weak transcription	Right Atrium	heart
2	chr17:19617600-19635400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr17:19619400-19624800	Enhancers	Esophagus	oesophagus
4	chr17:19619400-19625000	Enhancers	Fetal Muscle Leg	muscle
5	chr17:19619600-19625000	Enhancers	HMEC	breast
6	chr17:19619800-19627800	Enhancers	Fetal Intestine Large	intestine
7	chr17:19620000-19624800	Enhancers	HSMMtube	muscle
8	chr17:19620000-19628000	Enhancers	Fetal Intestine Small	intestine
9	chr17:19620200-19624800	Enhancers	Stomach Mucosa	stomach
10	chr17:19620400-19623800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:19620400-19625000	Enhancers	Colonic Mucosa	Colon
12	chr17:19620600-19627400	Weak transcription	Brain Anterior Caudate	brain
13	chr17:19620800-19623600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr17:19620800-19624800	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr17:19621200-19624800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr17:19621600-19624400	Enhancers	Placenta	Placenta
17	chr17:19621600-19624600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:19622200-19623600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr17:19622200-19624000	Enhancers	HepG2	liver
20	chr17:19622400-19624600	Enhancers	Ovary	ovary
21	chr17:19622600-19625000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:19622800-19624600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr17:19622800-19624800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:19622800-19624800	Enhancers	NHEK	skin
25	chr17:19623000-19623600	Flanking Active TSS	Spleen	Spleen
26	chr17:19623000-19624200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr17:19623000-19624800	Enhancers	Gastric	stomach
28	chr17:19623000-19624800	Enhancers	Lung	lung
29	chr17:19623000-19624800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr17:19623000-19625200	Enhancers	A549	lung
31	chr17:19623200-19624000	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr17:19623200-19624000	Enhancers	Small Intestine	intestine
33	chr17:19623200-19624400	Flanking Active TSS	Hela-S3	cervix
34	chr17:19623200-19624600	Enhancers	Pancreas	Pancrea
35	chr17:19623200-19624800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr17:19623200-19648400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr17:19623400-19624200	Enhancers	Fetal Lung	lung
38	chr17:19623400-19624400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr17:19623400-19624400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr17:19623400-19624400	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr17:19623400-19624600	Enhancers	Adipose Nuclei	Adipose
42	chr17:19623400-19624600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
43	chr17:19623400-19628000	Enhancers	Fetal Heart	heart

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