Variant report

Variant	rs533281338
Chromosome Location	chr9:43684989-43684990
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	JUND	chr9:43684686-43685427	A549	lung:	n/a	chr9:43684864-43684873
2	YY1	chr9:43684587-43685436	A549	lung:	n/a	chr9:43684857-43684868
3	POLR2A	chr9:43684669-43685402	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr9:43684355-43685531	A549	lung:	n/a	n/a
5	CTCF	chr9:43684940-43685090	A549	lung:	n/a	n/a
6	FOSL2	chr9:43684578-43685014	HepG2	liver:	n/a	chr9:43684864-43684873
7	POLR2A	chr9:43684471-43685504	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr9:43684654-43685388	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOXA2	chr9:43684679-43685228	A549	lung:	n/a	n/a
10	CTCF	chr9:43684493-43685134	A549	lung:	n/a	chr9:43684809-43684822 chr9:43684811-43684819
11	POLR2A	chr9:43684931-43685455	HUVEC	blood vessel:	n/a	n/a
12	SIN3AK20	chr9:43684800-43684995	HepG2	liver:	n/a	n/a
13	CTCF	chr9:43684714-43685003	K562	blood:	n/a	chr9:43684809-43684822 chr9:43684811-43684819
14	POLR2A	chr9:43684881-43685091	HUVEC	blood vessel:	n/a	n/a
15	CTCF	chr9:43684632-43685018	A549	lung:	n/a	chr9:43684809-43684822 chr9:43684811-43684819
16	NR3C1	chr9:43684499-43685247	A549	lung:	n/a	n/a
17	USF1	chr9:43684679-43685018	HepG2	liver:	n/a	chr9:43684859-43684875
18	TCF3	chr9:43684660-43685194	GM12878	blood:	n/a	n/a
19	HEY1	chr9:43684639-43685418	HepG2	liver:	n/a	chr9:43684856-43684871
20	RXRA	chr9:43684939-43685312	HepG2	liver:	n/a	n/a
21	POLR2A	chr9:43684585-43685394	A549	lung:	n/a	n/a
22	POLR2A	chr9:43684547-43685445	A549	lung:	n/a	n/a
23	TAF1	chr9:43684517-43685485	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr9:43684713-43685132	K562	blood:	n/a	chr9:43684809-43684822 chr9:43684811-43684819
25	POLR2A	chr9:43684925-43685251	Gliobla	brain:	n/a	n/a
26	SP1	chr9:43684607-43685443	A549	lung:	n/a	chr9:43684866-43684878 chr9:43684867-43684876 chr9:43684867-43684876 chr9:43684868-43684877 chr9:43684866-43684878
27	POLR2A	chr9:43684961-43685093	MCF10A-Er-Src	breast:	n/a	n/a
28	TAF1	chr9:43684725-43685381	HepG2	liver:	n/a	n/a
29	POLR2A	chr9:43684645-43685474	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr9:43684840-43684990	SAEC	small airway:	n/a	n/a
31	POLR2A	chr9:43684620-43685387	A549	lung:	n/a	n/a
32	CTCF	chr9:43684840-43684990	HMEC	breast:	n/a	n/a
33	HEY1	chr9:43684799-43685004	HepG2	liver:	n/a	chr9:43684856-43684871
34	CTCF	chr9:43684531-43685075	A549	lung:	n/a	chr9:43684809-43684822 chr9:43684811-43684819
35	CTCF	chr9:43684920-43685070	AoAF	blood vessel:	n/a	n/a
36	SP1	chr9:43684589-43685422	A549	lung:	n/a	chr9:43684866-43684878 chr9:43684867-43684876 chr9:43684867-43684876 chr9:43684868-43684877 chr9:43684866-43684878
37	POLR2A	chr9:43684879-43685254	A549	lung:	n/a	n/a
38	NR3C1	chr9:43684506-43685462	A549	lung:	n/a	n/a
39	POLR2A	chr9:43684597-43685391	A549	lung:	n/a	n/a
40	TAF1	chr9:43684591-43685449	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr9:43684886-43685098	HCT-116	colon:	n/a	n/a
42	FOXA2	chr9:43684530-43685438	A549	lung:	n/a	n/a

Variant related genes	Relation type
CNTNAP3B	TF binding region

Extended variants
information (count: 193 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:193 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893173	chr9:43034822-43998470	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv1829975	chr9:43045290-43831337	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1032639	chr9:43064834-43701826	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1025182	chr9:43064834-43705240	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1027611	chr9:43064834-43747241	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1027107	chr9:43064834-43776906	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1034498	chr9:43064834-43780897	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1019827	chr9:43064834-43790334	Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv1030625	chr9:43064834-43800174	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1033674	chr9:43127213-43776906	Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1016572	chr9:43127213-43800174	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv436621	chr9:43145796-44122367	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv1015998	chr9:43166976-43734207	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1020636	chr9:43166976-43795563	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1020348	chr9:43166976-43800174	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv515142	chr9:43315660-43785116	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
17	esv3584910	chr9:43315670-43795575	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
18	nsv442543	chr9:43315670-43795575	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
19	nsv1022920	chr9:43315962-43772038	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv1025263	chr9:43315962-43776906	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
21	nsv1022381	chr9:43315962-43780897	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv1030430	chr9:43315962-43790334	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
23	nsv1020786	chr9:43315962-43795563	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
24	nsv1031843	chr9:43315962-43800174	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
25	nsv1030874	chr9:43315962-44114860	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island lncRNA	16 gene(s)	inside rSNPs	diseases
26	nsv1021270	chr9:43315962-44145340	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island lncRNA	19 gene(s)	inside rSNPs	diseases
27	nsv1024462	chr9:43315962-44205637	Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island lncRNA	20 gene(s)	inside rSNPs	diseases
28	nsv893178	chr9:43321166-43737633	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
29	nsv893179	chr9:43321166-43998470	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island lncRNA	11 gene(s)	inside rSNPs	diseases
30	nsv533545	chr9:43386522-43686949	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
31	nsv533560	chr9:43386522-43704940	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
32	nsv1032238	chr9:43437359-43780897	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
33	nsv1025380	chr9:43437359-43800174	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
34	esv2761263	chr9:43437359-43800186	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
35	nsv1029200	chr9:43437359-44214733	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island lncRNA	16 gene(s)	inside rSNPs	diseases
36	nsv893181	chr9:43444135-43998470	Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
37	nsv1029527	chr9:43445985-43795563	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
38	nsv1029736	chr9:43445985-43800174	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
39	nsv916819	chr9:43468811-43836398	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
40	nsv893182	chr9:43504854-43734193	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
41	nsv893183	chr9:43504854-43998470	Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
42	nsv1027112	chr9:43505840-43776906	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
43	nsv1017282	chr9:43505840-43780897	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
44	nsv1026143	chr9:43505840-43790334	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
45	nsv1015336	chr9:43505840-43795563	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
46	nsv1018686	chr9:43505840-43800174	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
47	nsv1015727	chr9:43505840-44114860	Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island lncRNA	12 gene(s)	inside rSNPs	diseases
48	nsv1025269	chr9:43505840-44136778	Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	14 gene(s)	inside rSNPs	diseases
49	nsv1029217	chr9:43505840-44145340	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	15 gene(s)	inside rSNPs	diseases
50	nsv1027371	chr9:43505840-44273229	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:43684200-43685200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:43684200-43685200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr9:43684200-43685200	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr9:43684200-43685200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr9:43684200-43685200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:43684200-43685200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:43684200-43685200	Active TSS	Fetal Brain Female	brain
8	chr9:43684200-43686200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:43684200-43686400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:43684200-43687000	Active TSS	Right Ventricle	heart
11	chr9:43684200-43687000	Active TSS	A549	lung
12	chr9:43684200-43687200	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr9:43684400-43685200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr9:43684400-43685200	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr9:43684800-43685000	Active TSS	Colonic Mucosa	Colon
16	chr9:43684800-43685200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr9:43684800-43685200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:43684800-43685200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:43684800-43685200	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr9:43684800-43685200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:43684800-43685200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:43684800-43685200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:43684800-43685200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:43684800-43685200	Active TSS	Adipose Nuclei	Adipose
25	chr9:43684800-43685200	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr9:43684800-43685200	Active TSS	Psoas Muscle	Psoas
27	chr9:43684800-43685200	Active TSS	Osteobl	bone
28	chr9:43684800-43686400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:43684800-43686800	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr9:43684800-43687000	Active TSS	Stomach Smooth Muscle	stomach
31	chr9:43684800-43687200	Active TSS	HMEC	breast
32	chr9:43684800-43687200	Active TSS	HUVEC	blood vessel

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