Variant report

Variant	rs11657205
Chromosome Location	chr17:19623023-19623024
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	FOSL2	chr17:19622558-19623052	MCF-7	breast:	n/a	chr17:19622779-19622789 chr17:19622780-19622788 chr17:19622779-19622789 chr17:19622779-19622789
2	CTCF	chr17:19622777-19623056	NHEK	skin:	n/a	n/a
3	SP1	chr17:19622397-19623029	A549	lung:	n/a	chr17:19622960-19622969
4	ESR1	chr17:19622946-19624505	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
5	STAT1	chr17:19622158-19623229	Hela-S3	cervix:	n/a	chr17:19622817-19622826 chr17:19622319-19622331 chr17:19622816-19622825 chr17:19622815-19622826 chr17:19622672-19622680 chr17:19622814-19622822 chr17:19622767-19622778
6	EP300	chr17:19622981-19624687	ECC-1	luminal epithelium:	n/a	chr17:19623022-19623029
7	TEAD4	chr17:19623005-19624707	ECC-1	luminal epithelium:	n/a	n/a
8	TEAD4	chr17:19622607-19624645	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr17:19621815-19623285	A549	lung:	n/a	chr17:19622302-19622318 chr17:19622301-19622319 chr17:19622303-19622316
10	FOS	chr17:19622132-19623051	MCF10A-Er-Src	breast:	n/a	chr17:19622779-19622789 chr17:19622780-19622788 chr17:19622779-19622789 chr17:19622779-19622789
11	ZBTB7A	chr17:19622788-19624774	ECC-1	luminal epithelium:	n/a	chr17:19622910-19622918 chr17:19622983-19622997 chr17:19622984-19622998 chr17:19622911-19622919
12	FOSL2	chr17:19622341-19623112	A549	lung:	n/a	chr17:19622779-19622789 chr17:19622780-19622788 chr17:19622779-19622789 chr17:19622779-19622789
13	NFIC	chr17:19622613-19624764	ECC-1	luminal epithelium:	n/a	chr17:19624229-19624246 chr17:19624230-19624246
14	SP1	chr17:19622425-19623050	A549	lung:	n/a	chr17:19622960-19622969
15	TCF12	chr17:19622858-19624837	ECC-1	luminal epithelium:	n/a	chr17:19624809-19624816 chr17:19624811-19624818
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	NFIC	chr17:19622501-19624942	ECC-1	luminal epithelium:	n/a	chr17:19624229-19624246 chr17:19624230-19624246
20	STAT3	chr17:19622334-19623041	MCF10A-Er-Src	breast:	n/a	chr17:19622817-19622826 chr17:19622816-19622825 chr17:19622672-19622680 chr17:19622814-19622822 chr17:19622815-19622826
21	FOXM1	chr17:19622946-19624798	ECC-1	luminal epithelium:	n/a	n/a
22	MYC	chr17:19622168-19623065	MCF10A-Er-Src	breast:	n/a	chr17:19622675-19622685 chr17:19622569-19622578
23	STAT3	chr17:19622583-19623045	MCF10A-Er-Src	breast:	n/a	chr17:19622817-19622826 chr17:19622816-19622825 chr17:19622672-19622680 chr17:19622814-19622822 chr17:19622815-19622826
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

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	chr1:118155066..118155566-chr17:19622783..19623320,2	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
ENSG00000180638	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1042183	0.80[TSI][hapmap]
rs11204410	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11655302	0.83[EUR][1000 genomes]
rs11655989	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11656096	1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12601430	0.81[AMR][1000 genomes]
rs12945000	0.81[EUR][1000 genomes]
rs12948881	0.80[TSI][hapmap]
rs1989379	0.80[TSI][hapmap]
rs34834489	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3760486	0.80[TSI][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11657205	COPS3	cis	cerebellum	SCAN
rs11657205	FLJ36000	cis	parietal	SCAN
rs11657205	FLJ10847	cis	multi-tissue	Pritchard
rs11657205	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

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	chr17:19618200-19623200	Weak transcription	Pancreas	Pancrea
4	chr17:19619400-19624800	Enhancers	Esophagus	oesophagus
5	chr17:19619400-19625000	Enhancers	Fetal Muscle Leg	muscle
6	chr17:19619600-19625000	Enhancers	HMEC	breast
7	chr17:19619800-19627800	Enhancers	Fetal Intestine Large	intestine
8	chr17:19620000-19624800	Enhancers	HSMMtube	muscle
9	chr17:19620000-19628000	Enhancers	Fetal Intestine Small	intestine
10	chr17:19620200-19624800	Enhancers	Stomach Mucosa	stomach
11	chr17:19620400-19623800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr17:19620400-19625000	Enhancers	Colonic Mucosa	Colon
13	chr17:19620600-19623200	Enhancers	Duodenum Mucosa	Duodenum
14	chr17:19620600-19627400	Weak transcription	Brain Anterior Caudate	brain
15	chr17:19620800-19623600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr17:19620800-19624800	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr17:19621200-19623200	Weak transcription	Small Intestine	intestine
18	chr17:19621200-19624800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr17:19621400-19623400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr17:19621600-19624400	Enhancers	Placenta	Placenta
21	chr17:19621600-19624600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr17:19622000-19623200	Enhancers	Hela-S3	cervix
23	chr17:19622200-19623200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr17:19622200-19623600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr17:19622200-19624000	Enhancers	HepG2	liver
26	chr17:19622400-19624600	Enhancers	Ovary	ovary
27	chr17:19622600-19623200	Enhancers	Placenta Amnion	Placenta Amnion
28	chr17:19622600-19625000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr17:19622800-19624600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr17:19622800-19624800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:19622800-19624800	Enhancers	NHEK	skin
32	chr17:19623000-19623600	Flanking Active TSS	Spleen	Spleen
33	chr17:19623000-19624200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr17:19623000-19624800	Enhancers	Gastric	stomach
35	chr17:19623000-19624800	Enhancers	Lung	lung
36	chr17:19623000-19624800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr17:19623000-19625200	Enhancers	A549	lung

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