Variant report

Variant	rs541518180
Chromosome Location	chr9:137000384-137000385
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	TAF1	chr9:137000098-137001417	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr9:137000122-137001241	U87	brain:	n/a	n/a
3	POLR2A	chr9:137000267-137000782	PANC-1	pancreas:	n/a	n/a
4	NFIC	chr9:137000363-137000689	HepG2	liver:	n/a	n/a
5	POLR2A	chr9:136999908-137002325	Hela-S3	cervix:	n/a	n/a
6	UBTF	chr9:136999905-137001239	K562	blood:	n/a	n/a
7	TBP	chr9:137000373-137001257	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr9:136999899-137003166	HepG2	liver:	n/a	n/a
9	YY1	chr9:137000269-137000588	GM12891	blood:	n/a	chr9:137000546-137000557
10	POLR2A	chr9:137000281-137001310	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr9:136999821-137001428	K562	blood:	n/a	n/a
12	NRF1	chr9:137000175-137001385	GM12878	blood:	n/a	chr9:137000877-137000888 chr9:137000507-137000516 chr9:137001185-137001199 chr9:137001188-137001197 chr9:137001188-137001199 chr9:137001158-137001167 chr9:137001188-137001202
13	PML	chr9:137000236-137001333	GM12878	blood:	n/a	n/a
14	IRF1	chr9:136999999-137001295	K562	blood:	n/a	chr9:137001154-137001168
15	POLR2A	chr9:137000331-137002161	GM12878	blood:	n/a	n/a
16	HEY1	chr9:137000108-137001522	HepG2	liver:	n/a	chr9:137000546-137000561 chr9:137001328-137001343 chr9:137001359-137001374 chr9:137001202-137001217 chr9:137000612-137000627
17	ELF1	chr9:137000234-137001347	GM12878	blood:	n/a	n/a
18	POLR2A	chr9:136999710-137001492	K562	blood:	n/a	n/a
19	TBP	chr9:136999770-137001266	K562	blood:	n/a	n/a
20	STAT1	chr9:137000302-137001184	GM12878	blood:	n/a	n/a
21	YY1	chr9:137000216-137001551	HepG2	liver:	n/a	chr9:137000546-137000557 chr9:137001204-137001218 chr9:137001220-137001234 chr9:137001203-137001214 chr9:137001158-137001167 chr9:137001203-137001212 chr9:137001206-137001215
22	TAF1	chr9:137000165-137001404	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr9:137000193-137002010	GM19099	blood:	n/a	n/a
24	TAF1	chr9:137000255-137000946	HepG2	liver:	n/a	n/a
25	POLR2A	chr9:137000300-137000945	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr9:137000031-137001443	HepG2	liver:	n/a	n/a
27	POLR2A	chr9:137000202-137001903	HUVEC	blood vessel:	n/a	n/a
28	HCFC1	chr9:136999632-137002548	Hela-S3	cervix:	n/a	n/a
29	EBF1	chr9:137000376-137001009	GM12878	blood:	n/a	n/a
30	JUND	chr9:137000243-137000438	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr9:137000250-137001676	A549	lung:	n/a	n/a
32	POLR2A	chr9:137000313-137000906	A549	lung:	n/a	n/a
33	NRF1	chr9:137000231-137001496	SK-N-SH	brain:	n/a	chr9:137000877-137000888 chr9:137000507-137000516 chr9:137001185-137001199 chr9:137001188-137001197 chr9:137001188-137001199 chr9:137001158-137001167 chr9:137001188-137001202
34	POLR2A	chr9:136999748-137001441	ECC-1	luminal epithelium:	n/a	n/a
35	MAX	chr9:137000243-137001574	K562	blood:	n/a	n/a
36	MYC	chr9:137000114-137001788	Hela-S3	cervix:	n/a	n/a
37	MTA3	chr9:136999947-137001221	GM12878	blood:	n/a	n/a
38	IRF1	chr9:137000054-137001317	K562	blood:	n/a	chr9:137001154-137001168
39	RELA	chr9:137000241-137001288	GM15510	blood:	n/a	n/a
40	POLR2A	chr9:137000186-137001387	H1-hESC	embryonic stem cell:	n/a	n/a
41	KAP1	chr9:137000170-137001018	HEK293	kidney:	n/a	n/a
42	MAZ	chr9:136999891-137002028	IMR90	lung:	n/a	n/a
43	HEY1	chr9:137000346-137001385	K562	blood:	n/a	chr9:137000546-137000561 chr9:137001328-137001343 chr9:137001359-137001374 chr9:137001202-137001217 chr9:137000612-137000627
44	POLR2A	chr9:137000305-137001488	ProgFib	skin:	n/a	n/a
45	REST	chr9:137000117-137001231	HL-60	blood:	n/a	chr9:137000463-137000476 chr9:137001162-137001175 chr9:137000751-137000764
46	POLR2A	chr9:137000213-137000945	U87	brain:	n/a	n/a
47	POLR2A	chr9:137000091-137001435	GM12891	blood:	n/a	n/a
48	E2F4	chr9:137000188-137001267	MCF10A-Er-Src	breast:	n/a	chr9:137000507-137000516 chr9:137000592-137000604 chr9:137001189-137001198 chr9:137001043-137001054 chr9:137000460-137000470 chr9:137001206-137001215 chr9:137001158-137001167 chr9:137000620-137000630
49	HEY1	chr9:137000186-137001140	K562	blood:	n/a	chr9:137000546-137000561 chr9:137000612-137000627
50	YY1	chr9:137000225-137001397	GM12878	blood:	n/a	chr9:137000546-137000557 chr9:137001204-137001218 chr9:137001220-137001234 chr9:137001203-137001214 chr9:137001158-137001167 chr9:137001203-137001212 chr9:137001206-137001215

No.	Distal block	Cell Line	Cell type
1	chr16:401149..403748-chr9:137000262..137001904,2	MCF-7	breast:
2	chr9:136930118..136934023-chr9:136998387..137002829,10	K562	blood:
3	chr9:136931194..136934944-chr9:136998387..137002829,6	K562	blood:
4	chr9:136999027..137003702-chr9:137026566..137032835,8	MCF-7	breast:
5	chr9:136930108..136935337-chr9:136999374..137002737,14	MCF-7	breast:
6	chr9:136997943..137000936-chr9:137029556..137031957,3	K562	blood:
7	chr9:136919895..136922369-chr9:137000361..137002123,2	MCF-7	breast:
8	chr9:136999035..137002778-chr9:137027888..137031331,5	K562	blood:
9	chr9:136282958..136284963-chr9:136998714..137001684,2	K562	blood:
10	chr9:136928987..136935981-chr9:136998799..137005312,16	MCF-7	breast:
11	chr9:136999192..137001560-chr9:137216028..137218729,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BRD3-1	chr9:137000308-137000408	XLOC_007882
2	lnc-BRD3-1	chr9:137000308-137001037	XLOC_007882
3	lnc-BRD3-1	chr9:137000308-137000771	ENSG00000273249.1
4	lnc-BRD3-1	chr9:137000308-137000894	ENSG00000273249.1

Variant related genes	Relation type
WDR5	TF binding region
ENSG00000221676	Chromatin interaction
ENSG00000169925	Chromatin interaction
ENSG00000148300	Chromatin interaction
ENSG00000103126	Chromatin interaction
ENSG00000186350	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	esv3392543	chr9:137000156-137002904	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	esv3444727	chr9:137000331-137002454	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr9:136999400-137000400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:136999400-137000400	Flanking Active TSS	Hela-S3	cervix
3	chr9:136999400-137000400	Flanking Active TSS	HMEC	breast
4	chr9:136999400-137001600	Active TSS	Colonic Mucosa	Colon
5	chr9:136999600-137000400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:136999600-137000400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr9:136999600-137000400	Flanking Active TSS	Brain Anterior Caudate	brain
8	chr9:136999600-137000400	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr9:136999600-137000400	Flanking Active TSS	Brain Hippocampus Middle	brain
10	chr9:136999600-137000400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:136999600-137000400	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr9:136999600-137000400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr9:136999600-137000400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr9:136999600-137000400	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr9:136999600-137000400	Flanking Active TSS	Dnd41	blood
16	chr9:136999600-137000600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr9:136999600-137002000	Active TSS	Lung	lung
18	chr9:136999600-137002400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr9:136999800-137000400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:136999800-137000400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr9:136999800-137000400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr9:136999800-137000400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr9:136999800-137000400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:136999800-137000400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:136999800-137000400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr9:136999800-137000400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr9:136999800-137000400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr9:136999800-137000400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr9:136999800-137000400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr9:136999800-137000400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr9:136999800-137000400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr9:136999800-137000400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:136999800-137000400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:136999800-137000400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:136999800-137000400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:136999800-137000400	Flanking Active TSS	Liver	Liver
37	chr9:136999800-137000400	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr9:136999800-137000400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr9:136999800-137000400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr9:136999800-137000400	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr9:136999800-137000400	Flanking Active TSS	Fetal Stomach	stomach
42	chr9:136999800-137000400	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr9:136999800-137000400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr9:136999800-137000400	Flanking Active TSS	Stomach Mucosa	stomach
45	chr9:136999800-137000400	Flanking Active TSS	Thymus	Thymus
46	chr9:136999800-137000400	Flanking Active TSS	A549	lung
47	chr9:136999800-137000400	Flanking Active TSS	GM12878-XiMat	blood
48	chr9:136999800-137000400	Flanking Active TSS	K562	blood
49	chr9:136999800-137000600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:136999800-137000600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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