Variant report

Variant	rs12339669
Chromosome Location	chr9:117270304-117270305
allele	C/T
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	CTCF	chr9:117270065-117270320	A549	lung:	n/a	n/a
2	CTCF	chr9:117270068-117270304	NHEK	skin:	n/a	n/a
3	CTCF	chr9:117270061-117270310	Hela-S3	cervix:	n/a	n/a
4	CUX1	chr9:117270112-117270336	K562	blood:	n/a	n/a
5	CTCF	chr9:117269963-117270387	MCF-7	breast:	n/a	n/a
6	CTCF	chr9:117269980-117270388	GM12878	blood:	n/a	n/a
7	CTCF	chr9:117270052-117270396	K562	blood:	n/a	n/a
8	FOXA1	chr9:117269956-117270318	T-47D	breast:	n/a	n/a
9	CTCF	chr9:117269869-117270523	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr9:117269974-117270329	HepG2	liver:	n/a	chr9:117270172-117270184
11	CTCF	chr9:117269965-117270371	HepG2	liver:	n/a	n/a
12	SMC3	chr9:117270005-117270336	HepG2	liver:	n/a	n/a
13	CTCF	chr9:117270059-117270361	K562	blood:	n/a	n/a
14	CTCF	chr9:117269983-117270370	K562	blood:	n/a	n/a
15	ZNF143	chr9:117269989-117270352	GM12878	blood:	n/a	n/a
16	SMC3	chr9:117270039-117270352	K562	blood:	n/a	n/a
17	CTCF	chr9:117270048-117270323	Spleen_OC	spleen:	n/a	n/a
18	CTCF	chr9:117269966-117270317	T-47D	breast:	n/a	n/a
19	RAD21	chr9:117270060-117270327	K562	blood:	n/a	chr9:117270172-117270184
20	RAD21	chr9:117269886-117270352	GM12878	blood:	n/a	chr9:117270172-117270184
21	RAD21	chr9:117269802-117270398	MCF-7	breast:	n/a	chr9:117270172-117270184
22	CEBPB	chr9:117270121-117270945	H1-hESC	embryonic stem cell:	n/a	chr9:117270601-117270612 chr9:117270561-117270572
23	TEAD4	chr9:117269923-117270356	K562	blood:	n/a	n/a
24	MAFK	chr9:117270055-117270353	K562	blood:	n/a	n/a
25	CTCF	chr9:117269997-117270313	HepG2	liver:	n/a	n/a
26	RAD21	chr9:117269867-117270405	H1-hESC	embryonic stem cell:	n/a	chr9:117270172-117270184
27	RAD21	chr9:117270006-117270304	IMR90	lung:	n/a	chr9:117270172-117270184
28	RAD21	chr9:117269915-117270427	ECC-1	luminal epithelium:	n/a	chr9:117270172-117270184
29	CTCF	chr9:117270006-117270340	IMR90	lung:	n/a	n/a
30	RAD21	chr9:117269966-117270433	A549	lung:	n/a	chr9:117270172-117270184
31	FOXA1	chr9:117269903-117270383	T-47D	breast:	n/a	n/a
32	RAD21	chr9:117269987-117270355	H1-hESC	embryonic stem cell:	n/a	chr9:117270172-117270184
33	RAD21	chr9:117269969-117270329	GM12878	blood:	n/a	chr9:117270172-117270184
34	RAD21	chr9:117269937-117270400	SK-N-SH_RA	brain:	n/a	chr9:117270172-117270184
35	CTCF	chr9:117270050-117270314	MCF-7	breast:	n/a	n/a
36	CTCF	chr9:117269983-117270498	HCT-116	colon:	n/a	n/a
37	RAD21	chr9:117269931-117270307	H1-hESC	embryonic stem cell:	n/a	chr9:117270172-117270184
38	CTCF	chr9:117270200-117270350	HCT-116	colon:	n/a	n/a
39	CTCF	chr9:117270074-117270305	LNCaP	prostate:	n/a	n/a
40	ZNF143	chr9:117270045-117270380	K562	blood:	n/a	n/a
41	RAD21	chr9:117269940-117270346	ECC-1	luminal epithelium:	n/a	chr9:117270172-117270184
42	CTCF	chr9:117269904-117270444	HCT-116	colon:	n/a	n/a
43	RAD21	chr9:117269839-117270539	HCT-116	colon:	n/a	chr9:117270172-117270184
44	RAD21	chr9:117269865-117270453	MCF-7	breast:	n/a	chr9:117270172-117270184
45	WRNIP1	chr9:117270202-117270392	GM12878	blood:	n/a	n/a
46	SMC3	chr9:117270005-117270358	Hela-S3	cervix:	n/a	n/a
47	SMC3	chr9:117269974-117270388	GM12878	blood:	n/a	n/a
48	RAD21	chr9:117269972-117270384	HepG2	liver:	n/a	chr9:117270172-117270184
49	RAD21	chr9:117269928-117270444	A549	lung:	n/a	chr9:117270172-117270184
50	CTCF	chr9:117269992-117270383	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:117269640..117272592-chr9:117365792..117368000,2	MCF-7	breast:
2	chr9:117270178..117273118-chr9:117281523..117283492,2	MCF-7	breast:
3	chr9:117249371..117250397-chr9:117269698..117270686,4	MCF-7	breast:
4	chr9:117250011..117250679-chr9:117269579..117270625,3	MCF-7	breast:
5	chr9:117268041..117272317-chr9:117272688..117278380,7	K562	blood:
6	chr9:117270219..117273953-chr9:117274800..117277625,4	K562	blood:
7	chr9:117263907..117271703-chr9:117371218..117376768,10	MCF-7	breast:
8	chr9:117101534..117102049-chr9:117270024..117270719,2	MCF-7	breast:
9	chr9:117167587..117168592-chr9:117269657..117270304,4	MCF-7	breast:
10	chr9:117197169..117197704-chr9:117269622..117270725,3	MCF-7	breast:
11	chr9:117267834..117270703-chr9:117341838..117344791,2	MCF-7	breast:
12	chr9:117270094..117270690-chr9:117415535..117416447,3	MCF-7	breast:
13	chr9:115511935..115513721-chr9:117269588..117272587,2	MCF-7	breast:
14	chr9:117268190..117270565-chr9:117371736..117374593,3	MCF-7	breast:
15	chr9:117264226..117271307-chr9:117346303..117355535,28	MCF-7	breast:

Variant related genes	Relation type
DFNB31	TF binding region
ENSG00000148158	Chromatin interaction
ENSG00000226609	Chromatin interaction
ENSG00000157693	Chromatin interaction
ENSG00000136888	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10217748	1.00[ASW][hapmap]
rs10982234	1.00[ASW][hapmap]
rs12339210	1.00[ASW][hapmap]
rs12348878	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17232074	1.00[ASN][1000 genomes]
rs2031875	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs2274158	1.00[ASW][hapmap]
rs4978584	1.00[ASW][hapmap]
rs4979375	1.00[ASW][hapmap]
rs730646	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
4	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
6	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv1050991	chr9:116953739-117442999	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
8	nsv1046311	chr9:116953739-117447142	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv1051987	chr9:116955841-117453668	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
13	nsv466534	chr9:116956268-117455810	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv615234	chr9:116956268-117455810	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
15	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
16	nsv615235	chr9:116958144-117367061	ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
17	nsv615236	chr9:116958144-117455810	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
18	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
19	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
20	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
21	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
22	nsv1053756	chr9:116975934-117443031	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
23	nsv540204	chr9:116975934-117443031	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
24	nsv1047704	chr9:116978041-117399362	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
25	nsv540205	chr9:116978041-117399362	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
26	nsv530950	chr9:117009156-117399361	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
27	nsv916139	chr9:117009169-117399454	Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
28	nsv530951	chr9:117032675-117439804	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
29	nsv831693	chr9:117116450-117281895	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12339669	RDH16	trans	parietal	SCAN
rs12339669	HDHD3	cis	cerebellum	SCAN
rs12339669	KIF12	cis	parietal	SCAN
rs12339669	SLC46A2	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117268600-117274000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:117268600-117275400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:117269800-117270400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr9:117269800-117270400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
5	chr9:117269800-117270400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:117269800-117270400	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr9:117269800-117271000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
8	chr9:117269800-117271200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr9:117270000-117270600	Enhancers	Primary B cells from peripheral blood	blood
10	chr9:117270000-117270600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:117270000-117270800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:117270000-117270800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr9:117270000-117271000	Bivalent Enhancer	Fetal Thymus	thymus
14	chr9:117270000-117271200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr9:117270000-117271400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr9:117270000-117274400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:117270200-117270400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:117270200-117270400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:117270200-117270400	Bivalent Enhancer	HepG2	liver
20	chr9:117270200-117270600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:117270200-117270800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
22	chr9:117270200-117271400	Enhancers	HUES48 Cell Line	embryonic stem cell

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