Variant report

Variant	rs12352899
Chromosome Location	chr9:102669619-102669620
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:100)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:100 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr9:102668879-102669636	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr9:102668560-102669687	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:102668911-102669636	GM12891	blood:	n/a	n/a
4	HA-E2F1	chr9:102668966-102669845	MCF-7	breast:	n/a	n/a
5	POLR2A	chr9:102668670-102669651	GM12892	blood:	n/a	n/a
6	POLR2A	chr9:102668518-102669647	MCF-7	breast:	n/a	n/a
7	POLR2A	chr9:102668634-102669821	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr9:102668891-102669665	GM12891	blood:	n/a	n/a
9	RCOR1	chr9:102668492-102669733	K562	blood:	n/a	n/a
10	POLR2A	chr9:102668643-102669644	HEK293	kidney:	n/a	n/a
11	RUNX3	chr9:102668934-102669660	GM12878	blood:	n/a	n/a
12	POLR2A	chr9:102668660-102669624	Hela-S3	cervix:	n/a	n/a
13	BCLAF1	chr9:102668939-102669619	GM12878	blood:	n/a	n/a
14	ELF1	chr9:102668895-102669698	GM12878	blood:	n/a	chr9:102669452-102669465
15	ZEB1	chr9:102668523-102669653	HepG2	liver:	n/a	chr9:102668829-102668841 chr9:102669375-102669386 chr9:102668830-102668841 chr9:102668831-102668838
16	POLR2A	chr9:102668624-102669653	HepG2	liver:	n/a	n/a
17	POLR2A	chr9:102668898-102669766	HepG2	liver:	n/a	n/a
18	ELF1	chr9:102668886-102669735	MCF-7	breast:	n/a	chr9:102669452-102669465
19	POLR2A	chr9:102668759-102669647	K562	blood:	n/a	n/a
20	POLR2A	chr9:102668710-102669619	HepG2	liver:	n/a	n/a
21	POLR2A	chr9:102668768-102669695	HL-60	blood:	n/a	n/a
22	POLR2A	chr9:102668889-102669880	GM12878	blood:	n/a	n/a
23	GTF2F1	chr9:102669117-102669730	Hela-S3	cervix:	n/a	n/a
24	MAX	chr9:102668946-102669717	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr9:102668573-102669630	K562	blood:	n/a	n/a
26	POLR2A	chr9:102668686-102669626	GM19193	blood:	n/a	n/a
27	POLR2A	chr9:102668678-102669661	GM15510	blood:	n/a	n/a
28	POLR2A	chr9:102668441-102669783	SK-N-MC	brain:	n/a	n/a
29	NRF1	chr9:102668490-102669715	SK-N-SH	brain:	n/a	chr9:102668938-102668952 chr9:102668941-102668955 chr9:102668941-102668952 chr9:102668941-102668952
30	POLR2A	chr9:102668797-102669628	GM10847	blood:	n/a	n/a
31	STAT5A	chr9:102669216-102669654	GM12878	blood:	n/a	n/a
32	POLR2A	chr9:102668649-102670376	MCF10A-Er-Src	breast:	n/a	n/a
33	SIN3AK20	chr9:102667952-102669746	MCF-7	breast:	n/a	n/a
34	HDAC2	chr9:102668583-102669643	MCF-7	breast:	n/a	n/a
35	POLR2A	chr9:102668591-102669658	HCT-116	colon:	n/a	n/a
36	POLR2A	chr9:102668488-102670759	MCF10A-Er-Src	breast:	n/a	n/a
37	CBX3	chr9:102669192-102669798	K562	blood:	n/a	n/a
38	ZNF143	chr9:102668926-102669680	H1-hESC	embryonic stem cell:	n/a	n/a
39	ELF1	chr9:102669238-102669665	K562	blood:	n/a	chr9:102669452-102669465
40	POLR2A	chr9:102668705-102669645	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr9:102668706-102669648	MCF-7	breast:	n/a	n/a
42	FOXM1	chr9:102668891-102669680	GM12878	blood:	n/a	n/a
43	POLR2A	chr9:102668781-102669643	K562	blood:	n/a	n/a
44	GABPA	chr9:102669028-102669680	A549	lung:	n/a	n/a
45	POLR2A	chr9:102668548-102669834	GM12891	blood:	n/a	n/a
46	POLR2A	chr9:102668628-102669633	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr9:102668645-102669831	K562	blood:	n/a	n/a
48	PML	chr9:102668819-102669737	K562	blood:	n/a	n/a
49	MAX	chr9:102668880-102669647	SK-N-SH	brain:	n/a	n/a
50	E2F6	chr9:102668870-102669660	H1-hESC	embryonic stem cell:	n/a	chr9:102668942-102668951

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:102669613-102669663	A549	lung:	n/a
2	chr9:102669613-102669663	NH-A	brain:	n/a
3	chr9:102669613-102669663	LNCaP	prostate:	n/a
4	chr9:102669613-102669663	ovcar-3	ovarian:	n/a
5	chr9:102669613-102669663	BJ	skin:	n/a
6	chr9:102669613-102669663	HCF	heart:	n/a
7	chr9:102669613-102669663	RPTEC	kidney:	n/a
8	chr9:102669613-102669663	HepG2	liver:	n/a
9	chr9:102669613-102669663	HPAEpiC	pulmonary alveolar:	n/a
10	chr9:102669613-102669663	PANC-1	pancreas:	n/a
11	chr9:102669613-102669663	HL-60	blood:	n/a
12	chr9:102669613-102669663	Jurkat	blood:	n/a
13	chr9:102669613-102669663	AG10803	skin:	n/a
14	chr9:102669613-102669663	GM06990	blood:	n/a
15	chr9:102669613-102669663	SKMC	muscle:	n/a
16	chr9:102669613-102669663	Caco-2	colon:	n/a
17	chr9:102669613-102669663	SK-N-SH	brain:	n/a
18	chr9:102669613-102669663	AG09319	gingival:	n/a
19	chr9:102669613-102669663	HEK293	kidney:	embryo
20	chr9:102669613-102669663	T-47D	breast:	n/a
21	chr9:102669613-102669663	SAEC	small airway:	n/a
22	chr9:102669613-102669663	ProgFib	skin:	n/a
23	chr9:102669613-102669663	K562	blood:	n/a
24	chr9:102669613-102669663	HRCEpiC	kidney:	n/a
25	chr9:102669613-102669663	HIPEpiC	eye:	n/a
26	chr9:102669613-102669663	IMR90	lung:	fetal
27	chr9:102669613-102669663	HUVEC	blood vessel:	n/a
28	chr9:102669613-102669663	Hepatocyte	liver:	n/a
29	chr9:102669613-102669663	H1-hESC	embryonic stem cell:	embryo
30	chr9:102669613-102669663	HRPEpiC	eye:	n/a
31	chr9:102669613-102669663	AG04450	lung:	fetal
32	chr9:102669613-102669663	PFSK-1	brain:	n/a
33	chr9:102669613-102669663	GM12878	blood:	n/a
34	chr9:102669613-102669663	HCPEpiC	choroid plexus:	n/a
35	chr9:102669613-102669663	AoSMC	blood vessel:	n/a
36	chr9:102669613-102669663	SK-N-SH_RA	brain:	n/a
37	chr9:102669613-102669663	PrEC	prostate:	n/a
38	chr9:102669613-102669663	HMEC	breast:	n/a
39	chr9:102669613-102669663	HAEpiC	amniotic membrane:	n/a
40	chr9:102669613-102669663	GM12891	blood:	n/a
41	chr9:102669613-102669663	MCF-7	breast:	n/a
42	chr9:102669613-102669663	NHDF-neo	bronchial:	n/a
43	chr9:102669613-102669663	NT2-D1	testis:	n/a
44	chr9:102669613-102669663	HNPCEpiC	eye:	n/a
45	chr9:102669613-102669663	CMK	blood:	n/a
46	chr9:102669613-102669663	HCT-116	colon:	n/a
47	chr9:102669613-102669663	SK-N-MC	brain:	n/a
48	chr9:102669613-102669663	BE2_C	brain:	n/a
49	chr9:102669613-102669663	AG04449	skin:	fetal
50	chr9:102669613-102669663	AG09309	skin:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:102580555..102587852-chr9:102667958..102670918,11	MCF-7	breast:
2	chr9:102580574..102584384-chr9:102666062..102670667,9	K562	blood:
3	chr9:102580667..102584355-chr9:102667685..102671328,3	K562	blood:
4	chr19:56631872..56632543-chr9:102669033..102669852,2	Hela-S3	cervix:
5	chr9:102668724..102670876-chr9:102691785..102694126,2	MCF-7	breast:
6	chr9:102668815..102670753-chr9:102697540..102700821,3	K562	blood:
7	chr9:102668815..102670753-chr9:102698922..102700821,2	K562	blood:
8	chr9:102667836..102670748-chr9:102860445..102862735,2	K562	blood:
9	chr9:102580482..102589062-chr9:102666380..102672134,16	MCF-7	breast:
10	chr10:33293935..33294887-chr9:102668937..102669750,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000255145	TF binding region
ENSG00000255145	CpG island
ENSG00000254571	Chromatin interaction
ENSG00000237461	Chromatin interaction
ENSG00000150093	Chromatin interaction
ENSG00000119509	Chromatin interaction
ENSG00000023318	Chromatin interaction
ENSG00000136874	Chromatin interaction
ENSG00000119508	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10117638	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117828	0.93[ASN][1000 genomes]
rs10120103	0.93[ASN][1000 genomes]
rs10121601	0.92[ASN][1000 genomes]
rs10121880	0.93[ASN][1000 genomes]
rs10122128	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123261	0.93[ASN][1000 genomes]
rs10124366	0.81[ASN][1000 genomes]
rs10125981	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217337	0.93[ASN][1000 genomes]
rs10217366	0.93[ASN][1000 genomes]
rs10217692	0.93[ASN][1000 genomes]
rs10512268	0.93[ASN][1000 genomes]
rs1055187	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739791	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739792	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739793	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739794	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760698	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760699	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760700	0.93[ASN][1000 genomes]
rs10760704	0.93[ASN][1000 genomes]
rs10760705	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760706	0.93[ASN][1000 genomes]
rs10819705	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819706	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819707	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819711	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819712	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988919	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988920	0.92[ASN][1000 genomes]
rs1830454	0.93[ASN][1000 genomes]
rs1852863	0.93[ASN][1000 genomes]
rs1881751	0.90[ASN][1000 genomes]
rs1962051	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969577	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997367	0.93[ASN][1000 genomes]
rs1997368	0.93[ASN][1000 genomes]
rs2031035	0.93[ASN][1000 genomes]
rs2416935	0.93[ASN][1000 genomes]
rs2416936	0.85[ASN][1000 genomes]
rs2416937	0.93[ASN][1000 genomes]
rs2416938	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416940	0.93[ASN][1000 genomes]
rs2416941	0.93[ASN][1000 genomes]
rs2416942	0.93[ASN][1000 genomes]
rs2900224	0.92[ASN][1000 genomes]
rs3739794	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3983846	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4282626	0.93[ASN][1000 genomes]
rs4452862	0.93[ASN][1000 genomes]
rs4585797	0.93[ASN][1000 genomes]
rs4742777	0.93[ASN][1000 genomes]
rs4742778	0.93[ASN][1000 genomes]
rs4743370	0.93[ASN][1000 genomes]
rs6478987	0.93[ASN][1000 genomes]
rs6478988	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478990	0.93[ASN][1000 genomes]
rs7022208	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022999	0.93[ASN][1000 genomes]
rs7027619	0.93[ASN][1000 genomes]
rs7027813	0.95[ASN][1000 genomes]
rs7030388	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038506	0.93[ASN][1000 genomes]
rs7039716	0.93[ASN][1000 genomes]
rs7853264	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299335	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS 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 target site	51 gene(s)	inside rSNPs	diseases
5	esv3366813	chr9:102657446-102670065	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12352899	STX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102668000-102669800	Active TSS	Placenta Amnion	Placenta Amnion
2	chr9:102668200-102669800	Active TSS	Muscle Satellite Cultured Cells	--
3	chr9:102668200-102669800	Active TSS	Colon Smooth Muscle	Colon
4	chr9:102668200-102669800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr9:102668200-102670000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:102668200-102670000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr9:102668200-102670000	Active TSS	Fetal Intestine Small	intestine
8	chr9:102668200-102670000	Active TSS	Fetal Kidney	kidney
9	chr9:102668200-102670000	Active TSS	HSMMtube	muscle
10	chr9:102668200-102670200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:102668200-102670200	Active TSS	NHDF-Ad	bronchial
12	chr9:102668200-102670400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr9:102668400-102669800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr9:102668400-102669800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:102668400-102669800	Active TSS	Esophagus	oesophagus
16	chr9:102668400-102669800	Active TSS	Fetal Brain Female	brain
17	chr9:102668400-102669800	Active TSS	Fetal Heart	heart
18	chr9:102668400-102669800	Active TSS	Left Ventricle	heart
19	chr9:102668400-102669800	Active TSS	Lung	lung
20	chr9:102668400-102669800	Active TSS	Pancreas	Pancrea
21	chr9:102668400-102669800	Active TSS	HSMM	muscle
22	chr9:102668400-102670000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr9:102668400-102670000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:102668400-102670000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:102668400-102670000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:102668400-102670000	Active TSS	Fetal Brain Male	brain
27	chr9:102668400-102670000	Active TSS	Fetal Muscle Trunk	muscle
28	chr9:102668400-102670000	Active TSS	Right Atrium	heart
29	chr9:102668400-102670000	Active TSS	Right Ventricle	heart
30	chr9:102668400-102670000	Active TSS	NH-A	brain
31	chr9:102668400-102670200	Active TSS	NHLF	lung
32	chr9:102668400-102670400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:102668400-102670400	Active TSS	Fetal Intestine Large	intestine
34	chr9:102668600-102669800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr9:102668600-102669800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:102668600-102669800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:102668600-102669800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:102668600-102669800	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr9:102668600-102669800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr9:102668600-102669800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:102668600-102669800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:102668600-102669800	Active TSS	Aorta	Aorta
43	chr9:102668600-102669800	Active TSS	Brain Hippocampus Middle	brain
44	chr9:102668600-102669800	Active TSS	Brain Substantia Nigra	brain
45	chr9:102668600-102669800	Active TSS	Colonic Mucosa	Colon
46	chr9:102668600-102669800	Active TSS	Duodenum Mucosa	Duodenum
47	chr9:102668600-102669800	Active TSS	Placenta	Placenta
48	chr9:102668600-102669800	Active TSS	Gastric	stomach
49	chr9:102668600-102669800	Active TSS	Ovary	ovary
50	chr9:102668600-102669800	Active TSS	Small Intestine	intestine

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