Variant report

Variant	rs2010744
Chromosome Location	chr17:19623351-19623352
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	ESR1	chr17:19623121-19623770	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
2	NR3C1	chr17:19623246-19623764	A549	lung:	n/a	n/a
3	YY1	chr17:19623072-19624720	ECC-1	luminal epithelium:	n/a	n/a
4	MAX	chr17:19623035-19624610	ECC-1	luminal epithelium:	n/a	chr17:19624504-19624514
5	ESR1	chr17:19622946-19624505	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
6	ESR1	chr17:19623101-19624392	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
7	NR3C1	chr17:19623202-19623649	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr17:19622981-19624687	ECC-1	luminal epithelium:	n/a	chr17:19623022-19623029
9	TEAD4	chr17:19623005-19624707	ECC-1	luminal epithelium:	n/a	n/a
10	TEAD4	chr17:19622607-19624645	ECC-1	luminal epithelium:	n/a	n/a
11	NR3C1	chr17:19623266-19623620	ECC-1	luminal epithelium:	n/a	n/a
12	ZBTB7A	chr17:19622788-19624774	ECC-1	luminal epithelium:	n/a	chr17:19622910-19622918 chr17:19622983-19622997 chr17:19622984-19622998 chr17:19622911-19622919
13	NFIC	chr17:19622613-19624764	ECC-1	luminal epithelium:	n/a	chr17:19624229-19624246 chr17:19624230-19624246
14	TCF12	chr17:19622858-19624837	ECC-1	luminal epithelium:	n/a	chr17:19624809-19624816 chr17:19624811-19624818
15	YY1	chr17:19623152-19624566	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr17:19623016-19624864	ECC-1	luminal epithelium:	n/a	chr17:19624504-19624514
17	ESR1	chr17:19622971-19624446	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
18	EP300	chr17:19622762-19624918	ECC-1	luminal epithelium:	n/a	chr17:19623022-19623029
19	FOXM1	chr17:19623029-19624701	ECC-1	luminal epithelium:	n/a	n/a
20	NFIC	chr17:19622501-19624942	ECC-1	luminal epithelium:	n/a	chr17:19624229-19624246 chr17:19624230-19624246
21	ESR1	chr17:19623135-19623682	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
22	FOXM1	chr17:19622946-19624798	ECC-1	luminal epithelium:	n/a	n/a
23	TFAP2C	chr17:19622515-19624604	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr17:19623013-19624857	ECC-1	luminal epithelium:	n/a	chr17:19624809-19624816 chr17:19624811-19624818
25	ESR1	chr17:19622953-19624569	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
26	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	chr17:19616686..19619985-chr17:19620299..19623719,4	MCF-7	breast:
2	chr17:19550345..19551966-chr17:19622078..19623602,2	MCF-7	breast:
3	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
ENSG00000180638	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs118943	1.00[ASW][hapmap]
rs150122	1.00[ASW][hapmap]
rs157396	1.00[ASW][hapmap]
rs157398	1.00[AFR][1000 genomes]
rs157402	1.00[ASW][hapmap]
rs157405	1.00[AFR][1000 genomes]
rs172186	1.00[ASW][hapmap]
rs188138	1.00[ASW][hapmap]
rs205093	1.00[ASW][hapmap]
rs205107	1.00[ASW][hapmap]
rs205110	1.00[ASW][hapmap]
rs281332	1.00[ASW][hapmap]
rs281346	1.00[ASW][hapmap]
rs281351	1.00[ASW][hapmap]
rs3098903	1.00[AFR][1000 genomes]
rs4925043	1.00[ASW][hapmap]
rs6587203	1.00[ASW][hapmap]
rs917519	1.00[ASW][hapmap]

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

No data

Chromatin state (count:37 , 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	chr17:19621400-19623400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:19621600-19624400	Enhancers	Placenta	Placenta
18	chr17:19621600-19624600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr17:19622200-19623600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr17:19622200-19624000	Enhancers	HepG2	liver
21	chr17:19622400-19624600	Enhancers	Ovary	ovary
22	chr17:19622600-19625000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr17:19622800-19624600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:19622800-19624800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr17:19622800-19624800	Enhancers	NHEK	skin
26	chr17:19623000-19623600	Flanking Active TSS	Spleen	Spleen
27	chr17:19623000-19624200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr17:19623000-19624800	Enhancers	Gastric	stomach
29	chr17:19623000-19624800	Enhancers	Lung	lung
30	chr17:19623000-19624800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr17:19623000-19625200	Enhancers	A549	lung
32	chr17:19623200-19624000	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr17:19623200-19624000	Enhancers	Small Intestine	intestine
34	chr17:19623200-19624400	Flanking Active TSS	Hela-S3	cervix
35	chr17:19623200-19624600	Enhancers	Pancreas	Pancrea
36	chr17:19623200-19624800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr17:19623200-19648400	Weak transcription	Placenta Amnion	Placenta Amnion

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