Variant report

Variant	rs73488779
Chromosome Location	chr9:101018005-101018006
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	POLR2A	chr9:101017627-101018687	HCT-116	colon:	n/a	n/a
2	FOXP2	chr9:101017850-101018352	SK-N-MC	brain:	n/a	n/a
3	CTCF	chr9:101017922-101018110	Spleen_OC	spleen:	n/a	n/a
4	MYBL2	chr9:101017588-101018528	HepG2	liver:	n/a	n/a
5	YY1	chr9:101017791-101018517	HCT-116	colon:	n/a	chr9:101017923-101017932 chr9:101018119-101018141 chr9:101017923-101017937 chr9:101017929-101017943 chr9:101018117-101018136 chr9:101017926-101017935 chr9:101018122-101018130
6	POLR2A	chr9:101017804-101018585	A549	lung:	n/a	n/a
7	POLR2A	chr9:101017937-101018557	A549	lung:	n/a	n/a
8	TAF1	chr9:101017765-101018796	K562	blood:	n/a	n/a
9	SMC3	chr9:101017144-101018689	Hela-S3	cervix:	n/a	chr9:101017948-101017958
10	EGR1	chr9:101017511-101018769	HCT-116	colon:	n/a	chr9:101018051-101018064 chr9:101018050-101018065 chr9:101018052-101018063 chr9:101017921-101017934 chr9:101018052-101018061 chr9:101018052-101018062 chr9:101018046-101018068 chr9:101017921-101017934 chr9:101017926-101017936 chr9:101018052-101018062 chr9:101017924-101017934 chr9:101017920-101017935 chr9:101018051-101018064 chr9:101017924-101017933 chr9:101017921-101017935 chr9:101018051-101018064 chr9:101017921-101017934 chr9:101018051-101018064 chr9:101017921-101017934 chr9:101018050-101018064
11	MAX	chr9:101017385-101018695	MCF-7	breast:	n/a	chr9:101017920-101017930
12	MXI1	chr9:101017814-101018563	H1-hESC	embryonic stem cell:	n/a	n/a
13	EGR1	chr9:101017745-101018353	ECC-1	luminal epithelium:	n/a	chr9:101018051-101018064 chr9:101018050-101018065 chr9:101018052-101018063 chr9:101017921-101017934 chr9:101018052-101018061 chr9:101018052-101018062 chr9:101018046-101018068 chr9:101017921-101017934 chr9:101017926-101017936 chr9:101018052-101018062 chr9:101017924-101017934 chr9:101017920-101017935 chr9:101018051-101018064 chr9:101017924-101017933 chr9:101017921-101017935 chr9:101018051-101018064 chr9:101017921-101017934 chr9:101018051-101018064 chr9:101017921-101017934 chr9:101018050-101018064
14	POLR2A	chr9:101017768-101018866	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr9:101017929-101019265	K562	blood:	n/a	n/a
16	POLR2A	chr9:101017688-101018854	GM19193	blood:	n/a	n/a
17	CTCF	chr9:101017980-101018130	HRE	kidney:	n/a	n/a
18	TCF12	chr9:101017756-101018583	ECC-1	luminal epithelium:	n/a	chr9:101017916-101017923
19	PBX3	chr9:101017801-101018694	SK-N-SH	brain:	n/a	n/a
20	E2F6	chr9:101017842-101018590	A549	lung:	n/a	chr9:101018286-101018297 chr9:101017926-101017935
21	MAX	chr9:101017755-101018664	ECC-1	luminal epithelium:	n/a	chr9:101017920-101017930
22	RCOR1	chr9:101015503-101018858	IMR90	lung:	n/a	n/a
23	CTCF	chr9:101017960-101018210	GM12867	blood:	n/a	n/a
24	POLR2A	chr9:101017698-101019384	GM12892	blood:	n/a	n/a
25	TAF1	chr9:101017619-101018941	ECC-1	luminal epithelium:	n/a	n/a
26	TCF3	chr9:101017611-101018544	GM12878	blood:	n/a	chr9:101018088-101018101
27	GABPA	chr9:101017906-101018690	A549	lung:	n/a	chr9:101017926-101017935
28	ELF1	chr9:101017730-101018604	K562	blood:	n/a	chr9:101018094-101018103 chr9:101017924-101017936 chr9:101018093-101018104
29	TAF1	chr9:101017919-101018675	GM12878	blood:	n/a	n/a
30	POLR2A	chr9:101017739-101018602	A549	lung:	n/a	n/a
31	MYC	chr9:101017698-101018623	A549	lung:	n/a	chr9:101017920-101017930
32	CTCF	chr9:101017980-101018130	HAc	cerebellar:	n/a	n/a
33	POLR2A	chr9:101017415-101018793	MCF10A-Er-Src	breast:	n/a	n/a
34	RUNX3	chr9:101017743-101018996	GM12878	blood:	n/a	n/a
35	GABPA	chr9:101017748-101018748	MCF-7	breast:	n/a	chr9:101017926-101017935
36	ELK1	chr9:101017767-101018712	GM12878	blood:	n/a	n/a
37	TAF1	chr9:101017782-101018595	H1-hESC	embryonic stem cell:	n/a	n/a
38	REST	chr9:101017917-101018718	HL-60	blood:	n/a	chr9:101018024-101018037 chr9:101018531-101018538
39	POLR2A	chr9:101017819-101018595	A549	lung:	n/a	n/a
40	BHLHE40	chr9:101018003-101018582	K562	blood:	n/a	chr9:101018558-101018574 chr9:101018560-101018576
41	MAX	chr9:101017877-101018693	ECC-1	luminal epithelium:	n/a	chr9:101017920-101017930
42	MYC	chr9:101017350-101018579	MCF10A-Er-Src	breast:	n/a	chr9:101017920-101017930
43	POLR2A	chr9:101017785-101018625	GM12878	blood:	n/a	n/a
44	HDAC2	chr9:101017779-101018571	HepG2	liver:	n/a	n/a
45	CREB1	chr9:101017633-101018754	HepG2	liver:	n/a	n/a
46	SMARCB1	chr9:101017231-101019137	Hela-S3	cervix:	n/a	n/a
47	YY1	chr9:101017882-101018552	K562	blood:	n/a	chr9:101017923-101017932 chr9:101018119-101018141 chr9:101017923-101017937 chr9:101017929-101017943 chr9:101018117-101018136 chr9:101017926-101017935 chr9:101018122-101018130
48	POLR2A	chr9:101017331-101018893	MCF-7	breast:	n/a	n/a
49	STAT3	chr9:101017987-101018155	MCF10A-Er-Src	breast:	n/a	n/a
50	YY1	chr9:101017816-101018643	ECC-1	luminal epithelium:	n/a	chr9:101017923-101017932 chr9:101018119-101018141 chr9:101017923-101017937 chr9:101017929-101017943 chr9:101018117-101018136 chr9:101017926-101017935 chr9:101018122-101018130

No.	Distal block	Cell Line	Cell type
1	chr9:100934229..100937131-chr9:101015572..101018332,2	MCF-7	breast:
2	chr9:100818376..100820486-chr9:101016476..101019522,4	K562	blood:
3	chr9:100994373..100997197-chr9:101017981..101019934,2	MCF-7	breast:
4	chr9:100934290..100936965-chr9:101016512..101018556,3	K562	blood:
5	chr9:100744384..100747791-chr9:101014978..101019057,4	MCF-7	breast:
6	chr9:100818822..100821185-chr9:101017013..101019589,2	MCF-7	breast:
7	chr9:100837647..100840134-chr9:101017650..101020011,2	MCF-7	breast:
8	chr9:100683079..100687048-chr9:101015405..101020638,4	K562	blood:
9	chr9:100951866..100957184-chr9:101014234..101020511,10	K562	blood:
10	chr9:100954775..100957184-chr9:101014893..101018488,3	K562	blood:
11	chr9:100683337..100688322-chr9:101015638..101019207,5	MCF-7	breast:
12	chr9:100817689..100820206-chr9:101017310..101019410,4	MCF-7	breast:
13	chr9:100973089..100975981-chr9:101016778..101019724,3	MCF-7	breast:
14	chr9:100952914..100958060-chr9:101016344..101019894,9	MCF-7	breast:

Variant related genes	Relation type
TBC1D2	TF binding region
ENSG00000095383	Chromatin interaction
ENSG00000224001	Chromatin interaction
ENSG00000095380	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000106789	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10125738	0.84[EUR][1000 genomes]
rs12345664	0.84[EUR][1000 genomes]
rs16914245	1.00[EUR][1000 genomes]
rs16914425	1.00[EUR][1000 genomes]
rs2050575	0.84[EUR][1000 genomes]
rs57094433	1.00[EUR][1000 genomes]
rs57262924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57583651	1.00[EUR][1000 genomes]
rs58106044	1.00[EUR][1000 genomes]
rs58523842	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58811309	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59313219	1.00[EUR][1000 genomes]
rs60489972	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60522491	1.00[EUR][1000 genomes]
rs61349713	1.00[EUR][1000 genomes]
rs61752516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7032496	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7048858	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73488716	1.00[EUR][1000 genomes]
rs73488726	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73488743	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73488748	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73488767	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73488773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73488774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73488777	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73488785	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73488791	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73490716	1.00[EUR][1000 genomes]
rs73490724	1.00[EUR][1000 genomes]
rs73490729	1.00[EUR][1000 genomes]
rs73490751	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 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	chr9:101015200-101019000	Active TSS	HSMMtube	muscle
2	chr9:101015600-101019400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:101016000-101019400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr9:101016200-101019000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:101016400-101019000	Active TSS	Esophagus	oesophagus
6	chr9:101016400-101019000	Active TSS	HMEC	breast
7	chr9:101016400-101019000	Active TSS	NHEK	skin
8	chr9:101016600-101019000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:101016600-101019200	Active TSS	HSMM	muscle
10	chr9:101016600-101019600	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr9:101016800-101018400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:101016800-101019400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr9:101016800-101019600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr9:101017000-101018400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:101017000-101018800	Active TSS	Muscle Satellite Cultured Cells	--
16	chr9:101017000-101018800	Active TSS	Fetal Brain Female	brain
17	chr9:101017000-101019000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:101017000-101019000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:101017000-101019000	Active TSS	Small Intestine	intestine
20	chr9:101017000-101019000	Active TSS	A549	lung
21	chr9:101017000-101019000	Active TSS	NHLF	lung
22	chr9:101017000-101019200	Active TSS	Gastric	stomach
23	chr9:101017000-101019400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr9:101017000-101019400	Active TSS	Right Atrium	heart
25	chr9:101017200-101019000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:101017200-101019000	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr9:101017200-101019000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:101017200-101019000	Active TSS	Osteobl	bone
29	chr9:101017200-101019200	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr9:101017200-101019400	Active TSS	Aorta	Aorta
31	chr9:101017200-101019400	Active TSS	Psoas Muscle	Psoas
32	chr9:101017400-101018200	Active TSS	HepG2	liver
33	chr9:101017400-101018600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:101017400-101018800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:101017400-101018800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:101017400-101018800	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr9:101017400-101018800	Active TSS	Colonic Mucosa	Colon
38	chr9:101017400-101018800	Active TSS	Fetal Lung	lung
39	chr9:101017400-101018800	Active TSS	Placenta	Placenta
40	chr9:101017400-101018800	Active TSS	Stomach Mucosa	stomach
41	chr9:101017400-101019000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:101017400-101019000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr9:101017400-101019000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:101017400-101019000	Active TSS	Primary monocytes fromperipheralblood	blood
45	chr9:101017400-101019000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr9:101017400-101019000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:101017400-101019000	Active TSS	Brain Hippocampus Middle	brain
48	chr9:101017400-101019000	Active TSS	Brain Substantia Nigra	brain
49	chr9:101017400-101019000	Active TSS	Fetal Heart	heart
50	chr9:101017400-101019000	Active TSS	Ovary	ovary

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