Variant report

Variant	rs578029871
Chromosome Location	chr9:108006338-108006339
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	GATA3	chr9:108006297-108006936	T-47D	breast:	n/a	chr9:108006396-108006412
2	MAX	chr9:108006171-108007606	HepG2	liver:	n/a	chr9:108007445-108007455
3	KAP1	chr9:108006267-108006781	U2OS	brain:	n/a	n/a
4	NFIC	chr9:108006291-108006968	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr9:108006273-108006899	K562	blood:	n/a	n/a
6	EP300	chr9:108006307-108006965	T-47D	breast:	n/a	n/a
7	MBD4	chr9:108006252-108006891	HepG2	liver:	n/a	n/a
8	CEBPB	chr9:108006323-108006966	Hela-S3	cervix:	n/a	n/a
9	GABPA	chr9:108006266-108007017	MCF-7	breast:	n/a	chr9:108006752-108006761 chr9:108006777-108006786
10	POLR2A	chr9:108006185-108007086	U87	brain:	n/a	n/a
11	MAX	chr9:108006189-108007109	HCT-116	colon:	n/a	n/a
12	GABPA	chr9:108006303-108007005	SK-N-SH	brain:	n/a	chr9:108006752-108006761 chr9:108006777-108006786
13	USF2	chr9:108006304-108006769	Hela-S3	cervix:	n/a	n/a
14	BCLAF1	chr9:108006279-108006939	GM12878	blood:	n/a	chr9:108006667-108006680
15	POLR2A	chr9:108005996-108008364	GM12878	blood:	n/a	n/a
16	MAX	chr9:108006154-108007699	ECC-1	luminal epithelium:	n/a	chr9:108007445-108007455
17	SP4	chr9:108006237-108006911	H1-hESC	embryonic stem cell:	n/a	n/a
18	TBP	chr9:108006318-108006744	GM12878	blood:	n/a	n/a
19	GABPA	chr9:108006232-108006968	SK-N-SH	brain:	n/a	chr9:108006752-108006761 chr9:108006777-108006786
20	SIX5	chr9:108006063-108006936	A549	lung:	n/a	n/a
21	POLR2A	chr9:108006275-108007402	HL-60	blood:	n/a	n/a
22	ELF1	chr9:108006241-108006809	HepG2	liver:	n/a	n/a
23	POLR2A	chr9:108006257-108007053	HL-60	blood:	n/a	n/a
24	POLR2A	chr9:108006232-108008189	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr9:108006292-108006853	GM12892	blood:	n/a	n/a
26	EP300	chr9:108006336-108006938	A549	lung:	n/a	n/a
27	NFIC	chr9:108006242-108006900	GM12878	blood:	n/a	n/a
28	BRCA1	chr9:108006153-108006835	Hela-S3	cervix:	n/a	n/a
29	RCOR1	chr9:108006154-108007044	Hela-S3	cervix:	n/a	n/a
30	CEBPB	chr9:108006243-108006937	GM12878	blood:	n/a	n/a
31	ZNF143	chr9:108006296-108008092	GM12878	blood:	n/a	chr9:108007470-108007488
32	SP1	chr9:108006247-108006925	A549	lung:	n/a	chr9:108006563-108006570 chr9:108006753-108006762 chr9:108006752-108006761 chr9:108006751-108006763 chr9:108006753-108006762
33	TAF1	chr9:108006314-108008163	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAFK	chr9:108006233-108006856	Hela-S3	cervix:	n/a	n/a
35	REST	chr9:108006165-108008038	H1-neurons	neurons:	n/a	chr9:108007759-108007772
36	E2F6	chr9:108006298-108006931	H1-hESC	embryonic stem cell:	n/a	chr9:108006752-108006761 chr9:108006716-108006726 chr9:108006752-108006764 chr9:108006665-108006675
37	JUN	chr9:108006243-108007117	K562	blood:	n/a	n/a
38	NFIC	chr9:108006314-108006934	HepG2	liver:	n/a	n/a
39	BHLHE40	chr9:108006183-108007382	GM12878	blood:	n/a	n/a
40	RCOR1	chr9:108005675-108007466	IMR90	lung:	n/a	n/a
41	FOXA1	chr9:108006335-108007041	HepG2	liver:	n/a	n/a
42	POLR2A	chr9:108006304-108006926	SK-N-MC	brain:	n/a	n/a
43	NFIC	chr9:108006262-108007077	SK-N-SH	brain:	n/a	n/a
44	TCF12	chr9:108006338-108007065	ECC-1	luminal epithelium:	n/a	n/a
45	MYC	chr9:108006334-108007122	A549	lung:	n/a	n/a
46	MAZ	chr9:108006258-108008310	IMR90	lung:	n/a	chr9:108007828-108007838 chr9:108007445-108007455
47	EP300	chr9:108006174-108007110	MCF-7	breast:	n/a	n/a
48	MAZ	chr9:108006118-108007098	K562	blood:	n/a	n/a
49	TCF12	chr9:108006242-108007698	ECC-1	luminal epithelium:	n/a	n/a
50	MAX	chr9:108006179-108008163	A549	lung:	n/a	chr9:108007828-108007838 chr9:108007445-108007455

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	chr9:107687369..107691649-chr9:108006197..108009884,7	MCF-7	breast:
7	chr9:107986788..107989562-chr9:108004560..108006596,2	K562	blood:

Variant related genes	Relation type
SLC44A1	TF binding region
ENSG00000165029	Chromatin interaction
ENSG00000152082	Chromatin interaction
ENSG00000226334	Chromatin interaction
ENSG00000238208	Chromatin interaction
ENSG00000070214	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:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108003600-108006400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr9:108003800-108006400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:108003800-108006400	Enhancers	Placenta	Placenta
4	chr9:108004200-108006400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:108004200-108006600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
6	chr9:108004600-108006400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:108004600-108006600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:108004600-108006600	Flanking Active TSS	Osteobl	bone
9	chr9:108004800-108006600	Flanking Active TSS	HUVEC	blood vessel
10	chr9:108004800-108009400	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr9:108005000-108009200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:108005400-108006400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:108005400-108006600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr9:108005600-108006400	Weak transcription	Gastric	stomach
15	chr9:108005800-108006400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr9:108005800-108006400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:108005800-108006400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr9:108005800-108006600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:108005800-108006600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr9:108005800-108006600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:108006000-108006400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:108006000-108006400	Flanking Active TSS	Fetal Kidney	kidney
23	chr9:108006000-108006400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr9:108006000-108006400	Enhancers	Small Intestine	intestine
25	chr9:108006000-108006600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr9:108006000-108006600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr9:108006000-108006600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr9:108006000-108006600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr9:108006000-108006600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr9:108006000-108006600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr9:108006000-108006600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr9:108006000-108006600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:108006000-108006600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:108006000-108006600	Flanking Active TSS	Dnd41	blood
35	chr9:108006000-108006600	Flanking Active TSS	Hela-S3	cervix
36	chr9:108006000-108006600	Flanking Active TSS	NH-A	brain
37	chr9:108006000-108008000	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr9:108006000-108008400	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr9:108006000-108008600	Active TSS	A549	lung
40	chr9:108006200-108006400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr9:108006200-108006400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr9:108006200-108006400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr9:108006200-108006400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr9:108006200-108006400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr9:108006200-108006400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:108006200-108006400	Active TSS	Brain Angular Gyrus	brain
47	chr9:108006200-108006400	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr9:108006200-108006400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr9:108006200-108006400	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr9:108006200-108006400	Flanking Active TSS	Colonic Mucosa	Colon

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