Variant report

Variant	rs73410253
Chromosome Location	chr9:15552889-15552890
allele	A/C
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	RCOR1	chr9:15552334-15553228	GM12878	blood:	n/a	n/a
2	PML	chr9:15552586-15553247	MCF-7	breast:	n/a	n/a
3	MAZ	chr9:15552266-15553210	HepG2	liver:	n/a	chr9:15552994-15553004
4	POLR2A	chr9:15552438-15553864	U87	brain:	n/a	n/a
5	MAX	chr9:15551946-15553574	HCT-116	colon:	n/a	chr9:15552994-15553004
6	POLR2A	chr9:15552421-15553382	A549	lung:	n/a	n/a
7	MAZ	chr9:15551975-15553524	Hela-S3	cervix:	n/a	chr9:15552994-15553004
8	ZKSCAN1	chr9:15552169-15553235	Hela-S3	cervix:	n/a	n/a
9	TAF1	chr9:15552605-15553133	PFSK-1	brain:	n/a	n/a
10	TBL1XR1	chr9:15552634-15553885	GM12878	blood:	n/a	n/a
11	CTCF	chr9:15552779-15552986	Spleen_OC	spleen:	n/a	n/a
12	MYC	chr9:15552051-15553080	K562	blood:	n/a	chr9:15552994-15553004
13	E2F6	chr9:15552338-15553456	A549	lung:	n/a	chr9:15552993-15553005 chr9:15552584-15552594 chr9:15552879-15552888
14	POLR2A	chr9:15552244-15553753	GM19193	blood:	n/a	n/a
15	EGR1	chr9:15552565-15553001	ECC-1	luminal epithelium:	n/a	chr9:15552920-15552930 chr9:15552788-15552801 chr9:15552879-15552888 chr9:15552789-15552803
16	POLR2A	chr9:15552644-15553143	A549	lung:	n/a	n/a
17	CTCF	chr9:15552857-15552912	Kidney_OC	kidney:	n/a	n/a
18	POLR2A	chr9:15552599-15553180	SK-N-SH	brain:	n/a	n/a
19	E2F6	chr9:15552233-15553518	K562	blood:	n/a	chr9:15552993-15553005 chr9:15552584-15552594 chr9:15552879-15552888
20	POLR2A	chr9:15552589-15553117	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr9:15552571-15553446	Hela-S3	cervix:	n/a	n/a
22	EGR1	chr9:15552595-15553044	MCF-7	breast:	n/a	chr9:15552920-15552930 chr9:15552788-15552801 chr9:15552879-15552888 chr9:15552789-15552803
23	RFX5	chr9:15552847-15553000	K562	blood:	n/a	chr9:15552868-15552877
24	CEBPB	chr9:15552069-15553236	Hela-S3	cervix:	n/a	n/a
25	MYC	chr9:15552638-15553073	HepG2	liver:	n/a	chr9:15552994-15553004
26	POLR2A	chr9:15552512-15553678	SK-N-MC	brain:	n/a	n/a
27	SP1	chr9:15552011-15553609	A549	lung:	n/a	chr9:15553152-15553163 chr9:15553153-15553167
28	ELF1	chr9:15552518-15553653	GM12878	blood:	n/a	chr9:15553080-15553093
29	MYC	chr9:15551957-15553790	NB4	blood:	n/a	chr9:15552994-15553004
30	POLR2A	chr9:15552141-15553618	HepG2	liver:	n/a	n/a
31	MAX	chr9:15552101-15553549	HepG2	liver:	n/a	chr9:15552994-15553004
32	ELF1	chr9:15552351-15553677	GM12878	blood:	n/a	chr9:15553080-15553093
33	POLR2A	chr9:15552048-15553740	GM12878	blood:	n/a	n/a
34	POLR2A	chr9:15552349-15553544	A549	lung:	n/a	n/a
35	POLR2A	chr9:15552499-15553237	PFSK-1	brain:	n/a	n/a
36	PAX5	chr9:15552621-15553244	GM12878	blood:	n/a	n/a
37	REST	chr9:15551662-15553918	H1-neurons	neurons:	n/a	chr9:15553247-15553260 chr9:15552521-15552530 chr9:15553160-15553174
38	POLR2A	chr9:15552584-15553711	U87	brain:	n/a	n/a
39	SMC3	chr9:15551978-15553613	Hela-S3	cervix:	n/a	chr9:15553250-15553260
40	MAX	chr9:15552189-15553535	K562	blood:	n/a	chr9:15552994-15553004
41	CEBPD	chr9:15552551-15553007	HepG2	liver:	n/a	n/a
42	POLR2A	chr9:15552603-15553216	HepG2	liver:	n/a	n/a
43	SP1	chr9:15552842-15553553	H1-hESC	embryonic stem cell:	n/a	chr9:15553152-15553163 chr9:15553153-15553167
44	POLR2A	chr9:15552591-15553200	GM12891	blood:	n/a	n/a
45	MAX	chr9:15552017-15553170	A549	lung:	n/a	chr9:15552994-15553004
46	EGR1	chr9:15552859-15553406	H1-hESC	embryonic stem cell:	n/a	chr9:15553084-15553093 chr9:15552920-15552930 chr9:15552879-15552888
47	EP300	chr9:15552780-15552965	HepG2	liver:	n/a	n/a
48	BRCA1	chr9:15552681-15553468	GM12878	blood:	n/a	n/a
49	MYC	chr9:15552722-15552958	MCF-7	breast:	n/a	n/a
50	CHD2	chr9:15552273-15553413	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:61559649..61560247-chr9:15552431..15552962,2	Hela-S3	cervix:
2	chr9:15510875..15512396-chr9:15551516..15553319,2	MCF-7	breast:
3	chr9:15509318..15512022-chr9:15550389..15555494,9	MCF-7	breast:

Variant related genes	Relation type
CCDC171	TF binding region
ENSG00000134825	Chromatin interaction
ENSG00000168496	Chromatin interaction
ENSG00000207601	Chromatin interaction
ENSG00000164985	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12682808	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685082	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs16933316	0.84[ASN][1000 genomes]
rs16933348	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2277191	0.90[EUR][1000 genomes]
rs276452	0.85[ASN][1000 genomes]
rs55771541	0.90[EUR][1000 genomes]
rs56361298	0.83[ASN][1000 genomes]
rs57191285	0.89[ASN][1000 genomes]
rs57467578	0.83[ASN][1000 genomes]
rs57849124	0.87[ASN][1000 genomes]
rs59639757	0.90[EUR][1000 genomes]
rs62571021	0.89[ASN][1000 genomes]
rs62571022	0.83[ASN][1000 genomes]
rs62571023	0.83[ASN][1000 genomes]
rs62571024	0.83[ASN][1000 genomes]
rs6474950	0.84[AFR][1000 genomes]
rs7021778	0.97[AFR][1000 genomes]
rs73408328	0.83[ASN][1000 genomes]
rs73408340	0.87[ASN][1000 genomes]
rs73410238	0.83[AFR][1000 genomes]
rs73410242	0.83[AFR][1000 genomes]
rs73410254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73410286	0.97[AFR][1000 genomes]
rs73416209	0.84[AFR][1000 genomes]
rs73644655	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73644657	0.90[EUR][1000 genomes]
rs7846818	0.95[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7860283	0.97[AFR][1000 genomes]
rs7873842	0.87[AFR][1000 genomes]
rs906798	0.85[AFR][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	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3407839	chr9:15530438-15665653	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15551800-15553400	Active TSS	Fetal Muscle Trunk	muscle
2	chr9:15551800-15553800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr9:15551800-15553800	Active TSS	Brain Cingulate Gyrus	brain
4	chr9:15551800-15554200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:15551800-15554400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:15551800-15554400	Active TSS	Brain Angular Gyrus	brain
7	chr9:15551800-15554400	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr9:15551800-15554400	Active TSS	Fetal Brain Female	brain
9	chr9:15551800-15554600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr9:15551800-15554600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr9:15552000-15553200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:15552000-15553200	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr9:15552000-15553400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:15552000-15553400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:15552000-15553400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr9:15552000-15553400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr9:15552000-15553600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:15552000-15553600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:15552000-15553600	Active TSS	Primary T cells from cord blood	blood
20	chr9:15552000-15553600	Active TSS	Muscle Satellite Cultured Cells	--
21	chr9:15552000-15553600	Active TSS	Fetal Muscle Leg	muscle
22	chr9:15552000-15553600	Active TSS	HSMM	muscle
23	chr9:15552000-15553800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:15552000-15553800	Flanking Active TSS	Liver	Liver
25	chr9:15552000-15553800	Active TSS	Pancreas	Pancrea
26	chr9:15552000-15554000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr9:15552000-15554000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:15552000-15554000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:15552000-15554000	Active TSS	Brain Substantia Nigra	brain
30	chr9:15552000-15554000	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr9:15552000-15554000	Active TSS	Rectal Smooth Muscle	rectum
32	chr9:15552000-15554000	Active TSS	Right Atrium	heart
33	chr9:15552000-15554000	Active TSS	Stomach Smooth Muscle	stomach
34	chr9:15552000-15554000	Active TSS	HSMMtube	muscle
35	chr9:15552000-15554200	Active TSS	Brain Hippocampus Middle	brain
36	chr9:15552000-15554400	Active TSS	H9 Cell Line	embryonic stem cell
37	chr9:15552000-15554400	Active TSS	Thymus	Thymus
38	chr9:15552000-15554600	Active TSS	NHDF-Ad	bronchial
39	chr9:15552200-15553200	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr9:15552200-15553200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr9:15552200-15553200	Active TSS	Colonic Mucosa	Colon
42	chr9:15552200-15553200	Active TSS	Placenta	Placenta
43	chr9:15552200-15553400	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr9:15552200-15553400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:15552200-15553400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr9:15552200-15553400	Active TSS	Fetal Intestine Small	intestine
47	chr9:15552200-15553400	Active TSS	NH-A	brain
48	chr9:15552200-15553600	Active TSS	Colon Smooth Muscle	Colon
49	chr9:15552200-15553600	Active TSS	Fetal Heart	heart
50	chr9:15552200-15553600	Active TSS	Fetal Lung	lung

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