Variant report

Variant	rs7213388
Chromosome Location	chr17:19622506-19622507
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	RAD21	chr17:19622042-19622567	A549	lung:	n/a	chr17:19622299-19622318 chr17:19622303-19622317
2	RAD21	chr17:19622071-19622916	ECC-1	luminal epithelium:	n/a	chr17:19622655-19622674 chr17:19622299-19622318 chr17:19622303-19622317 chr17:19622715-19622727
3	FOS	chr17:19622160-19622971	MCF10A-Er-Src	breast:	n/a	chr17:19622779-19622789 chr17:19622780-19622788 chr17:19622779-19622789 chr17:19622779-19622789
4	CTCF	chr17:19622220-19622510	HEK293	kidney:	n/a	chr17:19622302-19622318 chr17:19622301-19622319 chr17:19622303-19622316
5	TCF12	chr17:19621978-19623014	A549	lung:	n/a	n/a
6	SP1	chr17:19622397-19623029	A549	lung:	n/a	chr17:19622960-19622969
7	FOS	chr17:19622326-19622967	MCF10A-Er-Src	breast:	n/a	chr17:19622779-19622789 chr17:19622780-19622788 chr17:19622779-19622789 chr17:19622779-19622789
8	RAD21	chr17:19622061-19622570	MCF-7	breast:	n/a	chr17:19622299-19622318 chr17:19622303-19622317
9	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
10	STAT3	chr17:19622276-19623017	MCF10A-Er-Src	breast:	n/a	chr17:19622817-19622826 chr17:19622319-19622331 chr17:19622816-19622825 chr17:19622672-19622680 chr17:19622814-19622822 chr17:19622815-19622826
11	ZNF143	chr17:19622368-19622528	Hela-S3	cervix:	n/a	n/a
12	SMC3	chr17:19622107-19622523	HepG2	liver:	n/a	chr17:19622303-19622317
13	MYC	chr17:19622142-19622883	MCF10A-Er-Src	breast:	n/a	chr17:19622675-19622685 chr17:19622569-19622578
14	CTCF	chr17:19622066-19622507	MCF-7	breast:	n/a	chr17:19622302-19622318 chr17:19622301-19622319 chr17:19622303-19622316
15	CTCF	chr17:19621815-19623285	A549	lung:	n/a	chr17:19622302-19622318 chr17:19622301-19622319 chr17:19622303-19622316
16	FOS	chr17:19622132-19623051	MCF10A-Er-Src	breast:	n/a	chr17:19622779-19622789 chr17:19622780-19622788 chr17:19622779-19622789 chr17:19622779-19622789
17	CTCF	chr17:19622400-19622550	A549	lung:	n/a	n/a
18	RAD21	chr17:19621966-19622571	HepG2	liver:	n/a	chr17:19622299-19622318 chr17:19622303-19622317
19	FOSL2	chr17:19622341-19623112	A549	lung:	n/a	chr17:19622779-19622789 chr17:19622780-19622788 chr17:19622779-19622789 chr17:19622779-19622789
20	RAD21	chr17:19621950-19622544	HCT-116	colon:	n/a	chr17:19622299-19622318 chr17:19622303-19622317
21	RAD21	chr17:19622149-19622579	A549	lung:	n/a	chr17:19622299-19622318 chr17:19622303-19622317
22	RAD21	chr17:19621981-19622641	A549	lung:	n/a	chr17:19622299-19622318 chr17:19622303-19622317
23	RFX5	chr17:19622248-19622614	HepG2	liver:	n/a	n/a
24	CTCF	chr17:19622380-19622530	GM06990	blood:	n/a	n/a
25	RAD21	chr17:19622081-19622597	MCF-7	breast:	n/a	chr17:19622299-19622318 chr17:19622303-19622317
26	SP1	chr17:19622425-19623050	A549	lung:	n/a	chr17:19622960-19622969
27	RAD21	chr17:19621939-19622522	H1-hESC	embryonic stem cell:	n/a	chr17:19622299-19622318 chr17:19622303-19622317
28	RAD21	chr17:19621998-19622528	H1-hESC	embryonic stem cell:	n/a	chr17:19622299-19622318 chr17:19622303-19622317
29	NFIC	chr17:19622501-19624942	ECC-1	luminal epithelium:	n/a	chr17:19624229-19624246 chr17:19624230-19624246
30	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
31	MYC	chr17:19622168-19623065	MCF10A-Er-Src	breast:	n/a	chr17:19622675-19622685 chr17:19622569-19622578
32	CTCF	chr17:19622400-19622550	AoAF	blood vessel:	n/a	n/a
33	RAD21	chr17:19621988-19622940	HCT-116	colon:	n/a	chr17:19622907-19622917 chr17:19622655-19622674 chr17:19622299-19622318 chr17:19622303-19622317 chr17:19622715-19622727

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	chr17:19616430..19618663-chr17:19620797..19622524,3	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: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12325921	0.89[AFR][1000 genomes]
rs35448501	1.00[AMR][1000 genomes]
rs7213030	0.89[AFR][1000 genomes]
rs9901772	0.89[AFR][1000 genomes]
rs9915956	0.81[AFR][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

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	chr17:19618200-19623200	Weak transcription	Pancreas	Pancrea
4	chr17:19619400-19622800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr17:19619400-19624800	Enhancers	Esophagus	oesophagus
6	chr17:19619400-19625000	Enhancers	Fetal Muscle Leg	muscle
7	chr17:19619600-19625000	Enhancers	HMEC	breast
8	chr17:19619800-19627800	Enhancers	Fetal Intestine Large	intestine
9	chr17:19620000-19624800	Enhancers	HSMMtube	muscle
10	chr17:19620000-19628000	Enhancers	Fetal Intestine Small	intestine
11	chr17:19620200-19624800	Enhancers	Stomach Mucosa	stomach
12	chr17:19620400-19623800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr17:19620400-19625000	Enhancers	Colonic Mucosa	Colon
14	chr17:19620600-19622600	Enhancers	Gastric	stomach
15	chr17:19620600-19622600	Weak transcription	Spleen	Spleen
16	chr17:19620600-19623200	Enhancers	Duodenum Mucosa	Duodenum
17	chr17:19620600-19627400	Weak transcription	Brain Anterior Caudate	brain
18	chr17:19620800-19623600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr17:19620800-19624800	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr17:19621200-19622600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr17:19621200-19623200	Weak transcription	Small Intestine	intestine
22	chr17:19621200-19624800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr17:19621400-19622800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr17:19621400-19623400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr17:19621600-19622600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr17:19621600-19624400	Enhancers	Placenta	Placenta
27	chr17:19621600-19624600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:19622000-19622800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr17:19622000-19622800	Flanking Active TSS	NHEK	skin
30	chr17:19622000-19623200	Enhancers	Hela-S3	cervix
31	chr17:19622200-19622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr17:19622200-19622800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr17:19622200-19623200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr17:19622200-19623600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr17:19622200-19624000	Enhancers	HepG2	liver
36	chr17:19622400-19622600	Flanking Active TSS	A549	lung
37	chr17:19622400-19624600	Enhancers	Ovary	ovary

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