Variant report

Variant	rs377019262
Chromosome Location	chr9:108006191-108006192
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	MAX	chr9:108006171-108007606	HepG2	liver:	n/a	chr9:108007445-108007455
2	POLR2A	chr9:108006185-108007086	U87	brain:	n/a	n/a
3	MAX	chr9:108006189-108007109	HCT-116	colon:	n/a	n/a
4	POLR2A	chr9:108005996-108008364	GM12878	blood:	n/a	n/a
5	MAX	chr9:108006154-108007699	ECC-1	luminal epithelium:	n/a	chr9:108007445-108007455
6	SIX5	chr9:108006063-108006936	A549	lung:	n/a	n/a
7	BRCA1	chr9:108006153-108006835	Hela-S3	cervix:	n/a	n/a
8	RCOR1	chr9:108006154-108007044	Hela-S3	cervix:	n/a	n/a
9	REST	chr9:108006165-108008038	H1-neurons	neurons:	n/a	chr9:108007759-108007772
10	BHLHE40	chr9:108006183-108007382	GM12878	blood:	n/a	n/a
11	RCOR1	chr9:108005675-108007466	IMR90	lung:	n/a	n/a
12	EP300	chr9:108006174-108007110	MCF-7	breast:	n/a	n/a
13	MAZ	chr9:108006118-108007098	K562	blood:	n/a	n/a
14	MAX	chr9:108006179-108008163	A549	lung:	n/a	chr9:108007828-108007838 chr9:108007445-108007455
15	REST	chr9:108006170-108006917	A549	lung:	n/a	n/a
16	KAP1	chr9:108004454-108007078	HEK293	kidney:	n/a	n/a
17	FOSL2	chr9:108006164-108006898	A549	lung:	n/a	n/a
18	TAF1	chr9:108006171-108007032	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr9:108006158-108006899	A549	lung:	n/a	n/a
20	CHD1	chr9:108005094-108008425	IMR90	lung:	n/a	chr9:108007384-108007391 chr9:108006753-108006763
21	CHD1	chr9:108006132-108006762	H1-hESC	embryonic stem cell:	n/a	n/a
22	RCOR1	chr9:108006135-108007068	GM12878	blood:	n/a	n/a
23	CBX3	chr9:108006125-108007159	HCT-116	colon:	n/a	n/a
24	CBX3	chr9:108006169-108006907	K562	blood:	n/a	n/a
25	FOXM1	chr9:108006189-108006883	GM12878	blood:	n/a	n/a
26	MTA3	chr9:108006118-108006901	GM12878	blood:	n/a	n/a
27	HCFC1	chr9:108006143-108008261	Hela-S3	cervix:	n/a	n/a
28	CBX3	chr9:108006154-108007059	HCT-116	colon:	n/a	n/a
29	RCOR1	chr9:108006166-108007401	K562	blood:	n/a	n/a
30	GABPA	chr9:108006111-108007060	MCF-7	breast:	n/a	chr9:108006752-108006761 chr9:108006777-108006786
31	ZNF143	chr9:108006187-108006913	H1-hESC	embryonic stem cell:	n/a	n/a
32	SIN3AK20	chr9:108006135-108008306	MCF-7	breast:	n/a	n/a
33	GABPA	chr9:108006163-108007063	HL-60	blood:	n/a	chr9:108006752-108006761 chr9:108006777-108006786
34	TCF12	chr9:108006072-108007046	A549	lung:	n/a	n/a
35	NFIC	chr9:108006190-108006978	ECC-1	luminal epithelium:	n/a	n/a
36	MYC	chr9:108005936-108007658	NB4	blood:	n/a	chr9:108007445-108007455
37	GABPA	chr9:108006163-108006908	A549	lung:	n/a	chr9:108006752-108006761 chr9:108006777-108006786
38	MYBL2	chr9:108006139-108006955	HepG2	liver:	n/a	n/a
39	GABPA	chr9:108006182-108006911	A549	lung:	n/a	chr9:108006752-108006761 chr9:108006777-108006786
40	POLR2A	chr9:108005232-108009600	PBDE	blood:	n/a	n/a
41	POLR2A	chr9:108006191-108007080	U87	brain:	n/a	n/a
42	GATA1	chr9:108005183-108007231	PBDE	blood:	n/a	chr9:108005818-108005828 chr9:108006396-108006412
43	POLR2A	chr9:108005828-108009363	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr9:108006171-108007282	HUVEC	blood vessel:	n/a	n/a
45	ZKSCAN1	chr9:108006049-108006837	Hela-S3	cervix:	n/a	n/a
46	MXI1	chr9:108006179-108006339	K562	blood:	n/a	n/a
47	REST	chr9:108006168-108006990	HL-60	blood:	n/a	n/a
48	MAX	chr9:108006106-108007113	HCT-116	colon:	n/a	n/a
49	MXI1	chr9:108006127-108008242	SK-N-SH	brain:	n/a	n/a
50	TCF12	chr9:108006189-108007248	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:107948857..107951560-chr9:108005097..108008240,3	MCF-7	breast:
2	chr9:108004369..108006903-chr9:108106116..108108591,2	MCF-7	breast:
3	chr9:108005319..108006844-chr9:108176651..108179101,2	MCF-7	breast:
4	chr2:130939236..130940096-chr9:108006055..108006614,2	NB4	blood:
5	chr9:108005738..108008360-chr9:108117762..108120177,2	MCF-7	breast:
6	chr9:107986788..107989562-chr9:108004560..108006596,2	K562	blood:

Variant related genes	Relation type
SLC44A1	TF binding region
ENSG00000238208	Chromatin interaction
ENSG00000070214	Chromatin interaction
ENSG00000152082	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046935	chr9:107414720-108028061	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv893690	chr9:107992706-108083485	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription 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	11 gene(s)	inside rSNPs	diseases
10	nsv893691	chr9:107994629-108020284	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3368118	chr9:108006181-108008254	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108002400-108006200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:108002600-108006200	Weak transcription	Left Ventricle	heart
3	chr9:108003200-108006200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:108003200-108006200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:108003200-108006200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:108003400-108006200	Enhancers	Brain Substantia Nigra	brain
7	chr9:108003600-108006200	Enhancers	HepG2	liver
8	chr9:108003600-108006400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr9:108003800-108006400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:108003800-108006400	Enhancers	Placenta	Placenta
11	chr9:108004000-108006200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:108004000-108006200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr9:108004000-108006200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:108004000-108006200	Enhancers	HSMM	muscle
15	chr9:108004200-108006200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr9:108004200-108006400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:108004200-108006600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr9:108004400-108006200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr9:108004600-108006200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:108004600-108006200	Active TSS	NHLF	lung
21	chr9:108004600-108006400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:108004600-108006600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:108004600-108006600	Flanking Active TSS	Osteobl	bone
24	chr9:108004800-108006200	Weak transcription	Fetal Brain Male	brain
25	chr9:108004800-108006200	Enhancers	Fetal Brain Female	brain
26	chr9:108004800-108006600	Flanking Active TSS	HUVEC	blood vessel
27	chr9:108004800-108009400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr9:108005000-108006200	Enhancers	Brain Anterior Caudate	brain
29	chr9:108005000-108006200	Weak transcription	Fetal Lung	lung
30	chr9:108005000-108006200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:108005000-108006200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr9:108005000-108009200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:108005200-108006200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr9:108005200-108006200	Weak transcription	Ovary	ovary
35	chr9:108005200-108006200	Weak transcription	Right Atrium	heart
36	chr9:108005200-108006200	Enhancers	Stomach Mucosa	stomach
37	chr9:108005400-108006200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:108005400-108006200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:108005400-108006200	Weak transcription	Aorta	Aorta
40	chr9:108005400-108006200	Enhancers	Fetal Thymus	thymus
41	chr9:108005400-108006200	Weak transcription	HSMMtube	muscle
42	chr9:108005400-108006200	Enhancers	K562	blood
43	chr9:108005400-108006400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:108005400-108006600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr9:108005600-108006200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:108005600-108006200	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr9:108005600-108006200	Enhancers	Adipose Nuclei	Adipose
48	chr9:108005600-108006200	Enhancers	Brain Cingulate Gyrus	brain
49	chr9:108005600-108006200	Weak transcription	Psoas Muscle	Psoas
50	chr9:108005600-108006200	Enhancers	NHEK	skin

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