Variant report

Variant	rs529058347
Chromosome Location	chr9:17578819-17578820
allele	A/C/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	MAX	chr9:17578691-17579412	Hela-S3	cervix:	n/a	n/a
2	CREB1	chr9:17578738-17579751	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr9:17578644-17579395	ECC-1	luminal epithelium:	n/a	n/a
4	ZNF143	chr9:17578790-17579563	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAF1	chr9:17578688-17579771	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr9:17578756-17579340	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr9:17578811-17579206	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr9:17578735-17579686	H1-hESC	embryonic stem cell:	n/a	chr9:17578919-17578933 chr9:17578852-17578865 chr9:17578921-17578935
9	REST	chr9:17578682-17579609	H1-neurons	neurons:	n/a	chr9:17578853-17578863
10	SUZ12	chr9:17578555-17579994	NT2-D1	testis:	n/a	n/a
11	MAX	chr9:17578717-17579374	A549	lung:	n/a	n/a
12	SMC3	chr9:17578699-17579862	Hela-S3	cervix:	n/a	n/a
13	MAX	chr9:17578610-17579756	H1-hESC	embryonic stem cell:	n/a	n/a
14	YY1	chr9:17578763-17579130	H1-hESC	embryonic stem cell:	n/a	chr9:17578848-17578859 chr9:17578771-17578780 chr9:17578766-17578780 chr9:17578852-17578866 chr9:17578763-17578777
15	RAD21	chr9:17578722-17579302	ECC-1	luminal epithelium:	n/a	chr9:17578919-17578933 chr9:17578852-17578865 chr9:17578921-17578935
16	ZNF143	chr9:17578817-17579257	Hela-S3	cervix:	n/a	n/a
17	MAX	chr9:17578693-17579747	ECC-1	luminal epithelium:	n/a	n/a
18	TCF12	chr9:17578703-17579319	ECC-1	luminal epithelium:	n/a	chr9:17578745-17578755
19	CREB1	chr9:17578652-17579375	H1-hESC	embryonic stem cell:	n/a	n/a
20	EP300	chr9:17578743-17579225	H1-hESC	embryonic stem cell:	n/a	chr9:17578852-17578868 chr9:17578853-17578869
21	CHD2	chr9:17578731-17579704	Hela-S3	cervix:	n/a	n/a
22	CHD2	chr9:17578780-17579235	H1-hESC	embryonic stem cell:	n/a	n/a
23	TCF7L2	chr9:17578784-17579607	Hela-S3	cervix:	n/a	n/a
24	USF2	chr9:17578640-17579179	H1-hESC	embryonic stem cell:	n/a	chr9:17578850-17578866 chr9:17578984-17579000
25	ZNF263	chr9:17578724-17579134	HEK293-T-REx	kidney:	n/a	n/a
26	E2F1	chr9:17578726-17579522	Hela-S3	cervix:	n/a	chr9:17579058-17579067 chr9:17579359-17579369 chr9:17579020-17579031 chr9:17579473-17579482 chr9:17578952-17578963 chr9:17578852-17578862 chr9:17578999-17579010 chr9:17579060-17579069
27	NFIC	chr9:17578778-17579193	ECC-1	luminal epithelium:	n/a	n/a
28	YY1	chr9:17578801-17579260	H1-hESC	embryonic stem cell:	n/a	chr9:17578848-17578859 chr9:17578852-17578866
29	MAX	chr9:17578592-17579891	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr9:17578812-17579851	H1-neurons	neurons:	n/a	n/a
31	RAD21	chr9:17578756-17579140	H1-hESC	embryonic stem cell:	n/a	chr9:17578919-17578933 chr9:17578852-17578865 chr9:17578921-17578935
32	RCOR1	chr9:17578565-17579698	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr9:17578704-17579831	Hela-S3	cervix:	n/a	n/a
34	SIN3A	chr9:17578811-17579732	H1-hESC	embryonic stem cell:	n/a	chr9:17578984-17578993 chr9:17578983-17578991
35	POLR2A	chr9:17578646-17579552	H1-hESC	embryonic stem cell:	n/a	n/a
36	E2F6	chr9:17578686-17579532	H1-hESC	embryonic stem cell:	n/a	chr9:17579058-17579067 chr9:17579359-17579369 chr9:17579473-17579482 chr9:17578852-17578862 chr9:17579060-17579069
37	TAF1	chr9:17578812-17579341	H1-neurons	neurons:	n/a	n/a
38	HA-E2F1	chr9:17578683-17579606	Hela-S3	cervix:	n/a	chr9:17579058-17579067 chr9:17579359-17579369 chr9:17579020-17579031 chr9:17579541-17579551 chr9:17579473-17579482 chr9:17578952-17578963 chr9:17578852-17578862 chr9:17578999-17579010 chr9:17579060-17579069
39	POLR2A	chr9:17578785-17579941	H1-neurons	neurons:	n/a	n/a
40	RAD21	chr9:17578725-17579085	H1-hESC	embryonic stem cell:	n/a	chr9:17578919-17578933 chr9:17578852-17578865 chr9:17578921-17578935
41	E2F6	chr9:17578483-17579540	H1-hESC	embryonic stem cell:	n/a	chr9:17579058-17579067 chr9:17579359-17579369 chr9:17579473-17579482 chr9:17578852-17578862 chr9:17579060-17579069
42	POLR2A	chr9:17578505-17579671	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTBP2	chr9:17578745-17579933	H1-hESC	embryonic stem cell:	n/a	n/a
44	TBP	chr9:17578636-17579700	H1-hESC	embryonic stem cell:	n/a	n/a
45	HCFC1	chr9:17578579-17579706	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr9:17578816-17579318	H1-hESC	embryonic stem cell:	n/a	n/a
47	CREB1	chr9:17578794-17579273	ECC-1	luminal epithelium:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:17578779-17578829	HL-60	blood:	n/a
2	chr9:17578779-17578829	HAEpiC	amniotic membrane:	n/a
3	chr9:17578779-17578829	HIPEpiC	eye:	n/a
4	chr9:17578779-17578829	HNPCEpiC	eye:	n/a
5	chr9:17578779-17578829	GM12892	blood:	n/a
6	chr9:17578779-17578829	IMR90	lung:	fetal
7	chr9:17578779-17578829	HepG2	liver:	n/a
8	chr9:17578779-17578829	H1-hESC	embryonic stem cell:	embryo
9	chr9:17578779-17578829	HPAEpiC	pulmonary alveolar:	n/a
10	chr9:17578779-17578829	ProgFib	skin:	n/a
11	chr9:17578779-17578829	GM12878	blood:	n/a
12	chr9:17578779-17578829	AoSMC	blood vessel:	n/a
13	chr9:17578779-17578829	SKMC	muscle:	n/a
14	chr9:17578779-17578829	Jurkat	blood:	n/a
15	chr9:17578779-17578829	BE2_C	brain:	n/a
16	chr9:17578779-17578829	AG09309	skin:	n/a
17	chr9:17578779-17578829	GM06990	blood:	n/a
18	chr9:17578779-17578829	NH-A	brain:	n/a
19	chr9:17578779-17578829	NHDF-neo	bronchial:	n/a
20	chr9:17578779-17578829	Caco-2	colon:	n/a
21	chr9:17578779-17578829	HCT-116	colon:	n/a
22	chr9:17578779-17578829	U87	brain:	n/a
23	chr9:17578779-17578829	PFSK-1	brain:	n/a
24	chr9:17578779-17578829	AG10803	skin:	n/a
25	chr9:17578779-17578829	AG04449	skin:	fetal
26	chr9:17578779-17578829	HCF	heart:	n/a
27	chr9:17578779-17578829	HCM	heart:	n/a
28	chr9:17578779-17578829	NHBE	bronchial:	n/a
29	chr9:17578779-17578829	SK-N-MC	brain:	n/a
30	chr9:17578779-17578829	HEK293	kidney:	embryo
31	chr9:17578779-17578829	NT2-D1	testis:	n/a
32	chr9:17578779-17578829	SAEC	small airway:	n/a
33	chr9:17578779-17578829	GM12891	blood:	n/a
34	chr9:17578779-17578829	HRPEpiC	eye:	n/a
35	chr9:17578779-17578829	BJ	skin:	n/a
36	chr9:17578779-17578829	CMK	blood:	n/a
37	chr9:17578779-17578829	A549	lung:	n/a
38	chr9:17578779-17578829	Hepatocyte	liver:	n/a
39	chr9:17578779-17578829	AG09319	gingival:	n/a
40	chr9:17578779-17578829	RPTEC	kidney:	n/a
41	chr9:17578779-17578829	HUVEC	blood vessel:	n/a
42	chr9:17578779-17578829	PANC-1	pancreas:	n/a
43	chr9:17578779-17578829	MCF-7	breast:	n/a
44	chr9:17578779-17578829	HMEC	breast:	n/a
45	chr9:17578779-17578829	ovcar-3	ovarian:	n/a
46	chr9:17578779-17578829	HCPEpiC	choroid plexus:	n/a
47	chr9:17578779-17578829	Hela-S3	cervix:	n/a
48	chr9:17578779-17578829	LNCaP	prostate:	n/a
49	chr9:17578779-17578829	HRCEpiC	kidney:	n/a
50	chr9:17578779-17578829	T-47D	breast:	n/a

Variant related genes	Relation type
SH3GL2	TF binding region
SH3GL2	CpG island

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv892671	chr9:17378776-17610211	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv2422265	chr9:17396711-17598187	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv517380	chr9:17564267-17633232	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv466274	chr9:17564267-17633232	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv613701	chr9:17564267-17633232	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv892672	chr9:17564267-17634566	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1025072	chr9:17577141-17632543	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv3414236	chr9:17577977-17580825	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17577800-17580000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr9:17578200-17579000	Bivalent/Poised TSS	Ovary	ovary
3	chr9:17578200-17580000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:17578200-17580600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr9:17578400-17579000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
6	chr9:17578400-17579000	Flanking Active TSS	Hela-S3	cervix
7	chr9:17578400-17579800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr9:17578400-17580000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
9	chr9:17578400-17580000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr9:17578400-17580000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr9:17578400-17580000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:17578400-17580000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
13	chr9:17578400-17580200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr9:17578400-17580200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr9:17578400-17580400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr9:17578400-17580800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:17578400-17580800	Active TSS	Fetal Brain Female	brain
18	chr9:17578600-17579000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:17578600-17579000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
20	chr9:17578600-17579000	Active TSS	Primary B cells from cord blood	blood
21	chr9:17578600-17579000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr9:17578600-17579000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:17578600-17579000	Enhancers	Fetal Brain Male	brain
24	chr9:17578600-17579000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
25	chr9:17578600-17579000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
26	chr9:17578600-17579000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
27	chr9:17578600-17579200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
28	chr9:17578600-17579200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
29	chr9:17578600-17579200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
30	chr9:17578600-17579200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr9:17578600-17579200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
32	chr9:17578600-17579200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
33	chr9:17578600-17579200	Flanking Active TSS	Right Ventricle	heart
34	chr9:17578600-17579200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
35	chr9:17578600-17579400	Bivalent/Poised TSS	Fetal Kidney	kidney
36	chr9:17578600-17579600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:17578600-17579600	Enhancers	Liver	Liver
38	chr9:17578600-17579600	Active TSS	Rectal Smooth Muscle	rectum
39	chr9:17578600-17579600	Bivalent Enhancer	Spleen	Spleen
40	chr9:17578600-17579600	Bivalent/Poised TSS	HSMMtube	muscle
41	chr9:17578600-17579600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
42	chr9:17578600-17579600	Flanking Bivalent TSS/Enh	NH-A	brain
43	chr9:17578600-17579800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr9:17578600-17579800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:17578600-17579800	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr9:17578600-17579800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr9:17578600-17579800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:17578600-17579800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:17578600-17579800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:17578600-17579800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin

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