Variant report

Variant	rs57254984
Chromosome Location	chr9:85678383-85678384
allele	C/T
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	TEAD4	chr9:85677311-85678463	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr9:85676725-85678551	A549	lung:	n/a	n/a
3	MAX	chr9:85676736-85678503	MCF-7	breast:	n/a	n/a
4	JUND	chr9:85677372-85678439	MCF-7	breast:	n/a	n/a
5	E2F6	chr9:85676937-85678416	H1-hESC	embryonic stem cell:	n/a	chr9:85677063-85677073 chr9:85677324-85677336 chr9:85677861-85677871 chr9:85677791-85677801
6	SIN3AK20	chr9:85677427-85678468	MCF-7	breast:	n/a	n/a
7	SIN3AK20	chr9:85676619-85678645	MCF-7	breast:	n/a	n/a
8	MAX	chr9:85677091-85678446	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr9:85676860-85678412	Hela-S3	cervix:	n/a	n/a
10	MAX	chr9:85676795-85678489	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr9:85676857-85678869	MCF10A-Er-Src	breast:	n/a	n/a
12	MAX	chr9:85676817-85678452	A549	lung:	n/a	n/a
13	POLR2A	chr9:85678035-85678757	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr9:85678062-85678695	H1-neurons	neurons:	n/a	n/a
15	RFX5	chr9:85676883-85678491	Hela-S3	cervix:	n/a	n/a
16	MAX	chr9:85677195-85678481	H1-hESC	embryonic stem cell:	n/a	n/a
17	GATA3	chr9:85677493-85678410	MCF-7	breast:	n/a	n/a
18	TEAD4	chr9:85677302-85678412	ECC-1	luminal epithelium:	n/a	n/a
19	TCF12	chr9:85676743-85678393	A549	lung:	n/a	n/a
20	ZNF263	chr9:85676840-85678395	HEK293-T-REx	kidney:	n/a	chr9:85678119-85678128
21	MAX	chr9:85676872-85678532	MCF-7	breast:	n/a	n/a
22	POLR2A	chr9:85676868-85678401	Hela-S3	cervix:	n/a	n/a
23	ZNF143	chr9:85677614-85678434	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr9:85677143-85678504	H1-hESC	embryonic stem cell:	n/a	n/a
25	GATA3	chr9:85677540-85678584	T-47D	breast:	n/a	n/a
26	TCF12	chr9:85676583-85678563	ECC-1	luminal epithelium:	n/a	n/a
27	NFIC	chr9:85676653-85678451	ECC-1	luminal epithelium:	n/a	chr9:85676953-85676970
28	GABPA	chr9:85677621-85678417	MCF-7	breast:	n/a	n/a
29	FOXA2	chr9:85677621-85678389	A549	lung:	n/a	n/a
30	E2F6	chr9:85676826-85678554	H1-hESC	embryonic stem cell:	n/a	chr9:85677063-85677073 chr9:85677324-85677336 chr9:85677861-85677871 chr9:85677791-85677801
31	ELF1	chr9:85677098-85678478	MCF-7	breast:	n/a	chr9:85677791-85677803
32	HA-E2F1	chr9:85676309-85678592	MCF-7	breast:	n/a	chr9:85677063-85677073 chr9:85677324-85677336 chr9:85677861-85677871 chr9:85677791-85677801
33	TCF12	chr9:85676746-85678453	ECC-1	luminal epithelium:	n/a	n/a
34	HDAC2	chr9:85676844-85678471	MCF-7	breast:	n/a	n/a
35	NFIC	chr9:85676594-85678491	ECC-1	luminal epithelium:	n/a	chr9:85676953-85676970
36	ELF1	chr9:85677539-85678458	MCF-7	breast:	n/a	chr9:85677791-85677803
37	EP300	chr9:85676658-85678606	ECC-1	luminal epithelium:	n/a	chr9:85677784-85677800
38	EP300	chr9:85677474-85678404	ECC-1	luminal epithelium:	n/a	chr9:85677784-85677800
39	NR2F2	chr9:85677210-85678407	MCF-7	breast:	n/a	n/a
40	EGR1	chr9:85677528-85678384	MCF-7	breast:	n/a	chr9:85678017-85678027 chr9:85677788-85677801 chr9:85677788-85677801 chr9:85677791-85677800 chr9:85677789-85677800 chr9:85677791-85677801 chr9:85677788-85677801
41	TCF12	chr9:85676761-85678619	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
RASEF	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10429640	1.00[EUR][1000 genomes]
rs17085992	1.00[EUR][1000 genomes]
rs55999203	1.00[EUR][1000 genomes]
rs57845461	1.00[EUR][1000 genomes]
rs58019119	1.00[EUR][1000 genomes]
rs58084620	1.00[EUR][1000 genomes]
rs58273828	1.00[EUR][1000 genomes]
rs58372258	0.88[AFR][1000 genomes]
rs7033636	0.83[AMR][1000 genomes]
rs7043342	1.00[AMR][1000 genomes]
rs73471429	0.83[AMR][1000 genomes]
rs73471442	1.00[AMR][1000 genomes]
rs73471448	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73651022	1.00[EUR][1000 genomes]
rs73651023	1.00[EUR][1000 genomes]
rs73651024	1.00[EUR][1000 genomes]
rs73651025	1.00[EUR][1000 genomes]
rs73651026	1.00[EUR][1000 genomes]
rs73651028	1.00[EUR][1000 genomes]
rs73651029	1.00[EUR][1000 genomes]
rs73651030	1.00[EUR][1000 genomes]
rs73651031	1.00[EUR][1000 genomes]
rs73651032	1.00[EUR][1000 genomes]
rs73651038	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1043722	chr9:85663674-85747562	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85674400-85679800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr9:85675400-85678600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
3	chr9:85675400-85678600	Active TSS	Pancreas	Pancrea
4	chr9:85676000-85679400	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr9:85676200-85678400	Bivalent/Poised TSS	NHLF	lung
6	chr9:85676200-85678600	Active TSS	Colonic Mucosa	Colon
7	chr9:85676200-85679000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr9:85676200-85679000	Active TSS	Rectal Smooth Muscle	rectum
9	chr9:85676400-85678400	Active TSS	Gastric	stomach
10	chr9:85676400-85678400	Bivalent/Poised TSS	Thymus	Thymus
11	chr9:85676600-85678400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:85676600-85678600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
13	chr9:85676600-85678800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr9:85676600-85679000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr9:85676600-85679000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr9:85676800-85678400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr9:85676800-85678400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:85676800-85678400	Active TSS	A549	lung
19	chr9:85676800-85678600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr9:85676800-85678600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:85676800-85678600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:85676800-85678600	Bivalent Enhancer	Fetal Brain Male	brain
23	chr9:85676800-85678600	Bivalent/Poised TSS	Small Intestine	intestine
24	chr9:85676800-85678600	Active TSS	Hela-S3	cervix
25	chr9:85676800-85679000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr9:85676800-85679000	Active TSS	Fetal Intestine Small	intestine
27	chr9:85677000-85678400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:85677000-85678400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:85677000-85678400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:85677000-85678400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:85677000-85678400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:85677000-85678400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:85677200-85678400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:85677200-85678400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:85677200-85678400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
36	chr9:85677200-85678400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:85677200-85678400	Bivalent Enhancer	Spleen	Spleen
38	chr9:85677200-85678600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:85677200-85679000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr9:85677400-85678400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:85677400-85678400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:85677400-85678400	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
43	chr9:85677400-85678400	Flanking Active TSS	HMEC	breast
44	chr9:85677400-85678600	Active TSS	H9 Cell Line	embryonic stem cell
45	chr9:85677400-85678600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:85677400-85678600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:85677400-85678600	Active TSS	Fetal Kidney	kidney
48	chr9:85677400-85679000	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr9:85677400-85679400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
50	chr9:85677600-85678400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle

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