Variant report

Variant	rs28578388
Chromosome Location	chr9:137000059-137000060
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:63)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:63 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:136999908-137002325	Hela-S3	cervix:	n/a	n/a
2	UBTF	chr9:136999905-137001239	K562	blood:	n/a	n/a
3	POLR2A	chr9:136999899-137003166	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:136999821-137001428	K562	blood:	n/a	n/a
5	IRF1	chr9:136999999-137001295	K562	blood:	n/a	chr9:137001154-137001168
6	POLR2A	chr9:136999710-137001492	K562	blood:	n/a	n/a
7	TBP	chr9:136999770-137001266	K562	blood:	n/a	n/a
8	POLR2A	chr9:137000031-137001443	HepG2	liver:	n/a	n/a
9	HCFC1	chr9:136999632-137002548	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr9:136999748-137001441	ECC-1	luminal epithelium:	n/a	n/a
11	CUX1	chr9:137000038-137000171	GM12878	blood:	n/a	n/a
12	MTA3	chr9:136999947-137001221	GM12878	blood:	n/a	n/a
13	IRF1	chr9:137000054-137001317	K562	blood:	n/a	chr9:137001154-137001168
14	MAZ	chr9:136999891-137002028	IMR90	lung:	n/a	n/a
15	POLR2A	chr9:136999915-137001445	K562	blood:	n/a	n/a
16	MAX	chr9:136999999-137000150	GM12878	blood:	n/a	n/a
17	MAX	chr9:136999774-137002094	HepG2	liver:	n/a	n/a
18	MYC	chr9:136999809-137002356	K562	blood:	n/a	n/a
19	TCF12	chr9:137000027-137001290	A549	lung:	n/a	n/a
20	RCOR1	chr9:136999759-137000114	K562	blood:	n/a	n/a
21	MXI1	chr9:136999981-137002268	IMR90	lung:	n/a	n/a
22	MAX	chr9:136999720-137002056	K562	blood:	n/a	n/a
23	POLR2A	chr9:136999871-137002175	MCF-7	breast:	n/a	n/a
24	POLR2A	chr9:136999884-137002568	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr9:136999613-137002232	K562	blood:	n/a	n/a
26	MAX	chr9:137000054-137002399	A549	lung:	n/a	n/a
27	POLR2A	chr9:136999999-137001421	PBDE	blood:	n/a	n/a
28	ELF1	chr9:136999890-137000321	K562	blood:	n/a	chr9:137000116-137000129
29	MXI1	chr9:136999865-137002450	SK-N-SH	brain:	n/a	chr9:136999911-136999920
30	ZNF263	chr9:137000030-137001083	HEK293-T-REx	kidney:	n/a	n/a
31	POLR2A	chr9:137000021-137001452	HCT-116	colon:	n/a	n/a
32	POLR2A	chr9:137000004-137000099	ProgFib	skin:	n/a	n/a
33	POLR2A	chr9:136999865-137001863	K562	blood:	n/a	n/a
34	POLR2A	chr9:136999868-137002154	Raji	blood:	n/a	n/a
35	POLR2A	chr9:137000000-137001884	GM18505	blood:	n/a	n/a
36	BHLHE40	chr9:136999827-137000401	K562	blood:	n/a	n/a
37	POLR2A	chr9:137000051-137001208	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr9:137000038-137001481	GM15510	blood:	n/a	n/a
39	E2F6	chr9:136999885-137002008	K562	blood:	n/a	chr9:137001611-137001618 chr9:137001255-137001266 chr9:137000507-137000516 chr9:137000592-137000604 chr9:137001189-137001198 chr9:137001611-137001618 chr9:137000460-137000470 chr9:137001206-137001215 chr9:137001611-137001618 chr9:137001331-137001341 chr9:137001158-137001167 chr9:137000620-137000630
40	POLR2A	chr9:136999707-137001287	K562	blood:	n/a	n/a
41	MAX	chr9:136999981-137002100	MCF-7	breast:	n/a	n/a
42	REST	chr9:136999855-137001465	H1-neurons	neurons:	n/a	chr9:137000463-137000476 chr9:137001162-137001175 chr9:137000751-137000764
43	MAX	chr9:136999916-137001480	HCT-116	colon:	n/a	n/a
44	TBP	chr9:136999933-137001188	Hela-S3	cervix:	n/a	n/a
45	UBTF	chr9:136999954-137002207	K562	blood:	n/a	n/a
46	POLR2A	chr9:136999923-137002462	Hela-S3	cervix:	n/a	n/a
47	MAX	chr9:136999962-137001927	HCT-116	colon:	n/a	n/a
48	TBL1XR1	chr9:136999926-137001171	K562	blood:	n/a	n/a
49	MAX	chr9:137000029-137002283	Hela-S3	cervix:	n/a	n/a
50	JUND	chr9:136999830-137001309	GM12878	blood:	n/a	chr9:137001159-137001168

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:137000014-137000064	HCT-116	colon:	n/a
2	chr9:137000014-137000064	HMEC	breast:	n/a
3	chr9:137000014-137000064	NHBE	bronchial:	n/a
4	chr9:137000014-137000064	AG09309	skin:	n/a
5	chr9:137000014-137000064	IMR90	lung:	fetal
6	chr9:137000014-137000064	A549	lung:	n/a
7	chr9:137000014-137000064	HPAEpiC	pulmonary alveolar:	n/a
8	chr9:137000014-137000064	K562	blood:	n/a
9	chr9:137000014-137000064	BJ	skin:	n/a
10	chr9:137000014-137000064	AG04450	lung:	fetal
11	chr9:137000014-137000064	GM12891	blood:	n/a
12	chr9:137000014-137000064	Jurkat	blood:	n/a
13	chr9:137000014-137000064	HAEpiC	amniotic membrane:	n/a
14	chr9:137000014-137000064	MCF-7	breast:	n/a
15	chr9:137000014-137000064	Hepatocyte	liver:	n/a
16	chr9:137000014-137000064	AG10803	skin:	n/a
17	chr9:137000014-137000064	HRPEpiC	eye:	n/a
18	chr9:137000014-137000064	HIPEpiC	eye:	n/a
19	chr9:137000014-137000064	HEEpiC	esophagus:	n/a
20	chr9:137000014-137000064	HCF	heart:	n/a
21	chr9:137000014-137000064	HNPCEpiC	eye:	n/a
22	chr9:137000014-137000064	AG09319	gingival:	n/a
23	chr9:137000014-137000064	HL-60	blood:	n/a
24	chr9:137000014-137000064	Hela-S3	cervix:	n/a
25	chr9:137000014-137000064	HRCEpiC	kidney:	n/a
26	chr9:137000014-137000064	PFSK-1	brain:	n/a
27	chr9:137000014-137000064	NT2-D1	testis:	n/a
28	chr9:137000014-137000064	HepG2	liver:	n/a
29	chr9:137000014-137000064	HCPEpiC	choroid plexus:	n/a
30	chr9:137000014-137000064	NH-A	brain:	n/a
31	chr9:137000014-137000064	PrEC	prostate:	n/a
32	chr9:137000014-137000064	HCM	heart:	n/a
33	chr9:137000014-137000064	NB4	blood:	n/a
34	chr9:137000014-137000064	AG04449	skin:	fetal
35	chr9:137000014-137000064	ProgFib	skin:	n/a
36	chr9:137000014-137000064	RPTEC	kidney:	n/a
37	chr9:137000014-137000064	BE2_C	brain:	n/a
38	chr9:137000014-137000064	SKMC	muscle:	n/a
39	chr9:137000014-137000064	NHDF-neo	bronchial:	n/a
40	chr9:137000014-137000064	LNCaP	prostate:	n/a
41	chr9:137000014-137000064	T-47D	breast:	n/a
42	chr9:137000014-137000064	MCF10A-Er-Src	breast:	n/a
43	chr9:137000014-137000064	GM12892	blood:	n/a
44	chr9:137000014-137000064	GM12878	blood:	n/a
45	chr9:137000014-137000064	GM19239	blood:	n/a
46	chr9:137000014-137000064	PANC-1	pancreas:	n/a
47	chr9:137000014-137000064	SK-N-MC	brain:	n/a
48	chr9:137000014-137000064	HUVEC	blood vessel:	n/a
49	chr9:137000014-137000064	AoSMC	blood vessel:	n/a
50	chr9:137000014-137000064	Caco-2	colon:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136930118..136934023-chr9:136998387..137002829,10	K562	blood:
2	chr9:136931194..136934944-chr9:136998387..137002829,6	K562	blood:
3	chr9:136999027..137003702-chr9:137026566..137032835,8	MCF-7	breast:
4	chr9:136930108..136935337-chr9:136999374..137002737,14	MCF-7	breast:
5	chr9:136997943..137000936-chr9:137029556..137031957,3	K562	blood:
6	chr9:136999035..137002778-chr9:137027888..137031331,5	K562	blood:
7	chr9:136282958..136284963-chr9:136998714..137001684,2	K562	blood:
8	chr9:136928987..136935981-chr9:136998799..137005312,16	MCF-7	breast:
9	chr9:136999192..137001560-chr9:137216028..137218729,4	MCF-7	breast:

No data

Variant related genes	Relation type
WDR5	TF binding region
WDR5	CpG island
ENSG00000186350	Chromatin interaction
ENSG00000148300	Chromatin interaction
ENSG00000169925	Chromatin interaction
ENSG00000221676	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10118703	0.83[AMR][1000 genomes]
rs28523906	0.85[AMR][1000 genomes]
rs28572025	0.85[AMR][1000 genomes]
rs28626222	0.85[AMR][1000 genomes]
rs28637077	0.85[AMR][1000 genomes]
rs28637761	0.85[AMR][1000 genomes]
rs28657551	0.85[AMR][1000 genomes]
rs28726357	0.85[AMR][1000 genomes]
rs58124205	0.85[AMR][1000 genomes]
rs58734062	0.85[AMR][1000 genomes]
rs6479641	0.83[AMR][1000 genomes]
rs73663023	1.00[AMR][1000 genomes]
rs73663199	0.83[AMR][1000 genomes]
rs73663200	0.85[AMR][1000 genomes]
rs7860235	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv6751	chr9:136967475-137007131	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 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	chr9:136999200-137000200	Flanking Active TSS	Pancreas	Pancrea
2	chr9:136999200-137000200	Flanking Active TSS	NHEK	skin
3	chr9:136999400-137000200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:136999400-137000400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:136999400-137000400	Flanking Active TSS	Hela-S3	cervix
6	chr9:136999400-137000400	Flanking Active TSS	HMEC	breast
7	chr9:136999400-137001600	Active TSS	Colonic Mucosa	Colon
8	chr9:136999600-137000200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:136999600-137000200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr9:136999600-137000200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:136999600-137000200	Flanking Active TSS	Brain Angular Gyrus	brain
12	chr9:136999600-137000200	Flanking Active TSS	Colon Smooth Muscle	Colon
13	chr9:136999600-137000200	Flanking Active TSS	Fetal Brain Female	brain
14	chr9:136999600-137000200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr9:136999600-137000400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:136999600-137000400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr9:136999600-137000400	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr9:136999600-137000400	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr9:136999600-137000400	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr9:136999600-137000400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:136999600-137000400	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr9:136999600-137000400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr9:136999600-137000400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr9:136999600-137000400	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr9:136999600-137000400	Flanking Active TSS	Dnd41	blood
26	chr9:136999600-137000600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr9:136999600-137002000	Active TSS	Lung	lung
28	chr9:136999600-137002400	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr9:136999800-137000200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:136999800-137000200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr9:136999800-137000200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr9:136999800-137000200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:136999800-137000200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:136999800-137000200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:136999800-137000200	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr9:136999800-137000200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:136999800-137000200	Enhancers	Aorta	Aorta
38	chr9:136999800-137000200	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr9:136999800-137000200	Flanking Active TSS	Fetal Heart	heart
40	chr9:136999800-137000200	Flanking Active TSS	Fetal Intestine Large	intestine
41	chr9:136999800-137000200	Flanking Active TSS	Right Ventricle	heart
42	chr9:136999800-137000200	Enhancers	Small Intestine	intestine
43	chr9:136999800-137000400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:136999800-137000400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr9:136999800-137000400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr9:136999800-137000400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr9:136999800-137000400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:136999800-137000400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:136999800-137000400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr9:136999800-137000400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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