Variant report

Variant	rs59828051
Chromosome Location	chr9:21803165-21803166
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	MYC	chr9:21802516-21803418	HUVEC	blood vessel:	n/a	chr9:21802967-21802977
2	MAX	chr9:21802218-21803556	HUVEC	blood vessel:	n/a	chr9:21802967-21802977
3	SMC3	chr9:21803156-21803543	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr9:21801872-21804039	PANC-1	pancreas:	n/a	n/a
5	MTA3	chr9:21802862-21803279	GM12878	blood:	n/a	n/a
6	SIN3AK20	chr9:21803098-21803549	PFSK-1	brain:	n/a	n/a
7	MAX	chr9:21801967-21803842	HepG2	liver:	n/a	chr9:21802967-21802977
8	RAD21	chr9:21803104-21803503	IMR90	lung:	n/a	n/a
9	POLR2A	chr9:21802470-21803592	GM12878	blood:	n/a	n/a
10	MAFK	chr9:21803116-21803597	HepG2	liver:	n/a	n/a
11	POLR2A	chr9:21802055-21803938	HepG2	liver:	n/a	n/a
12	MAFK	chr9:21803116-21803612	HepG2	liver:	n/a	n/a
13	POLR2A	chr9:21801886-21803912	SK-N-MC	brain:	n/a	n/a
14	CHD2	chr9:21802051-21803486	GM12878	blood:	n/a	n/a
15	MAX	chr9:21802187-21803760	H1-hESC	embryonic stem cell:	n/a	chr9:21802967-21802977
16	MXI1	chr9:21802172-21803628	Hela-S3	cervix:	n/a	n/a
17	USF1	chr9:21803096-21803506	H1-hESC	embryonic stem cell:	n/a	n/a
18	USF1	chr9:21803083-21803468	A549	lung:	n/a	n/a
19	YY1	chr9:21802451-21803227	GM12878	blood:	n/a	n/a
20	POLR2A	chr9:21802951-21803440	HUVEC	blood vessel:	n/a	n/a
21	MXI1	chr9:21802117-21803802	GM12878	blood:	n/a	n/a
22	SIN3AK20	chr9:21803163-21803397	HepG2	liver:	n/a	n/a
23	RELA	chr9:21802380-21803410	GM18951	blood:	n/a	n/a
24	POLR2A	chr9:21802361-21803440	GM12892	blood:	n/a	n/a
25	TBP	chr9:21803096-21803439	Hela-S3	cervix:	n/a	n/a
26	MXI1	chr9:21803070-21803575	H1-hESC	embryonic stem cell:	n/a	n/a
27	REST	chr9:21801964-21803586	A549	lung:	n/a	chr9:21802327-21802340
28	USF2	chr9:21803117-21803436	HepG2	liver:	n/a	n/a
29	POLR2A	chr9:21801981-21803679	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr9:21801950-21803643	PFSK-1	brain:	n/a	n/a
31	HCFC1	chr9:21801475-21804210	Hela-S3	cervix:	n/a	n/a
32	BCLAF1	chr9:21802237-21803665	GM12878	blood:	n/a	chr9:21803052-21803065
33	E2F6	chr9:21802005-21803337	A549	lung:	n/a	chr9:21803191-21803201
34	MAX	chr9:21801861-21803572	ECC-1	luminal epithelium:	n/a	chr9:21802967-21802977
35	POLR2A	chr9:21802469-21803322	A549	lung:	n/a	n/a
36	MYC	chr9:21802503-21803385	MCF-7	breast:	n/a	chr9:21802967-21802977
37	BCLAF1	chr9:21802276-21803522	GM12878	blood:	n/a	chr9:21803052-21803065
38	BRCA1	chr9:21803114-21803364	Hela-S3	cervix:	n/a	n/a
39	ZNF263	chr9:21801422-21803458	HEK293-T-REx	kidney:	n/a	chr9:21801626-21801635 chr9:21802599-21802608
40	POLR2A	chr9:21801752-21803870	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr9:21803081-21803334	HepG2	liver:	n/a	n/a
42	MAFF	chr9:21803117-21803606	HepG2	liver:	n/a	n/a
43	TAF1	chr9:21803100-21803408	GM12891	blood:	n/a	n/a
44	MAX	chr9:21802266-21803952	GM12878	blood:	n/a	chr9:21802967-21802977
45	POLR2A	chr9:21801614-21803661	HCT-116	colon:	n/a	n/a
46	SPI1	chr9:21803044-21803377	GM12891	blood:	n/a	n/a
47	POLR2A	chr9:21802373-21803461	GM12878	blood:	n/a	n/a
48	RELA	chr9:21802423-21803533	GM15510	blood:	n/a	n/a
49	SIN3A	chr9:21801644-21803997	H1-hESC	embryonic stem cell:	n/a	chr9:21802588-21802601
50	GABPA	chr9:21801833-21803656	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:149858070..149858646-chr9:21802522..21803492,2	Hela-S3	cervix:
2	chr10:65280669..65281593-chr9:21802930..21803555,2	HCT-116	colon:
3	chr9:21802179..21803949-chr9:21994356..21995893,2	MCF-7	breast:
4	chr9:21801607..21803714-chr9:21992951..21995865,2	MCF-7	breast:

Variant related genes	Relation type
MTAP	TF binding region
ENSG00000184260	Chromatin interaction
ENSG00000240498	Chromatin interaction
ENSG00000147889	Chromatin interaction
ENSG00000165476	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000266446	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1440994	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58005508	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59397155	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60465887	1.00[EUR][1000 genomes]
rs7027003	1.00[EUR][1000 genomes]
rs7041147	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7041757	1.00[EUR][1000 genomes]
rs73429337	1.00[EUR][1000 genomes]
rs73429360	1.00[EUR][1000 genomes]
rs73429364	1.00[EUR][1000 genomes]
rs73649991	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1026981	chr9:21748202-21811697	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
3	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21801000-21803400	Active TSS	Stomach Smooth Muscle	stomach
2	chr9:21801400-21803800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr9:21801400-21804200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr9:21801400-21804400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr9:21801400-21804400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:21801400-21804400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:21801600-21803200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:21801600-21803400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:21801600-21803400	Active TSS	Fetal Brain Female	brain
10	chr9:21801600-21803800	Active TSS	Left Ventricle	heart
11	chr9:21801600-21803800	Active TSS	Pancreas	Pancrea
12	chr9:21801600-21804000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr9:21801600-21804000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr9:21801600-21804000	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr9:21801600-21804000	Active TSS	Ovary	ovary
16	chr9:21801600-21804000	Active TSS	Psoas Muscle	Psoas
17	chr9:21801600-21804200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:21801600-21804200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:21801600-21804200	Active TSS	Right Atrium	heart
20	chr9:21801600-21804400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr9:21801600-21804600	Active TSS	HSMMtube	muscle
22	chr9:21801600-21805000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:21801600-21805000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:21801800-21803200	Active TSS	Brain Angular Gyrus	brain
25	chr9:21801800-21803400	Active TSS	Fetal Stomach	stomach
26	chr9:21801800-21803600	Active TSS	Aorta	Aorta
27	chr9:21801800-21803600	Active TSS	Esophagus	oesophagus
28	chr9:21801800-21803600	Active TSS	Lung	lung
29	chr9:21801800-21803800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:21801800-21803800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr9:21801800-21803800	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr9:21801800-21803800	Active TSS	Placenta Amnion	Placenta Amnion
33	chr9:21801800-21804000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr9:21801800-21804000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:21801800-21804000	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr9:21801800-21804000	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr9:21801800-21804000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr9:21801800-21804000	Active TSS	Right Ventricle	heart
39	chr9:21801800-21804000	Active TSS	Stomach Mucosa	stomach
40	chr9:21801800-21804000	Active TSS	NHDF-Ad	bronchial
41	chr9:21801800-21804200	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr9:21801800-21804200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:21801800-21804200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:21801800-21804200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:21801800-21804200	Active TSS	Thymus	Thymus
46	chr9:21801800-21804400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:21801800-21804400	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr9:21801800-21804400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:21802000-21803200	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr9:21802000-21803200	Active TSS	Rectal Mucosa Donor 31	rectum

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