Variant report

Variant	rs561857543
Chromosome Location	chr9:3524505-3524506
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	MAX	chr9:3524473-3524912	NB4	blood:	n/a	chr9:3524737-3524747
2	POLR2A	chr9:3524442-3529266	GM12891	blood:	n/a	n/a
3	POLR2A	chr9:3520146-3530139	MCF10A-Er-Src	breast:	n/a	n/a
4	RCOR1	chr9:3524465-3524923	GM12878	blood:	n/a	n/a
5	NFIC	chr9:3524432-3525017	GM12878	blood:	n/a	n/a
6	ATF2	chr9:3524505-3525038	GM12878	blood:	n/a	n/a
7	EP300	chr9:3524388-3524938	K562	blood:	n/a	chr9:3524456-3524470
8	BHLHE40	chr9:3524430-3524925	GM12878	blood:	n/a	n/a
9	SIN3A	chr9:3524488-3527318	GM12878	blood:	n/a	chr9:3525124-3525133
10	CHD1	chr9:3524393-3527671	IMR90	lung:	n/a	chr9:3524990-3525000 chr9:3526447-3526457 chr9:3526442-3526452
11	SIN3A	chr9:3524486-3527356	H1-hESC	embryonic stem cell:	n/a	chr9:3525124-3525133
12	IRF1	chr9:3524340-3524919	K562	blood:	n/a	chr9:3524710-3524730 chr9:3524457-3524471 chr9:3524459-3524472 chr9:3524711-3524728 chr9:3524712-3524726 chr9:3524461-3524471 chr9:3524712-3524723
13	ZNF384	chr9:3524360-3524924	GM12878	blood:	n/a	n/a
14	EBF1	chr9:3524479-3524806	GM12878	blood:	n/a	n/a
15	BCLAF1	chr9:3524371-3524958	GM12878	blood:	n/a	chr9:3524461-3524470
16	POLR2A	chr9:3523584-3529804	MCF10A-Er-Src	breast:	n/a	n/a
17	CUX1	chr9:3524347-3524823	K562	blood:	n/a	n/a
18	POLR2A	chr9:3524489-3528155	GM19099	blood:	n/a	n/a
19	POLR2A	chr9:3524470-3529021	GM12878	blood:	n/a	n/a
20	MAZ	chr9:3524291-3527504	IMR90	lung:	n/a	chr9:3524987-3524997 chr9:3524737-3524747 chr9:3526414-3526424
21	POLR2A	chr9:3524465-3528199	IMR90	lung:	n/a	n/a
22	MXI1	chr9:3524347-3525182	GM12878	blood:	n/a	n/a
23	POLR2A	chr9:3524485-3525276	K562	blood:	n/a	n/a
24	POLR2A	chr9:3524417-3524995	GM12892	blood:	n/a	n/a
25	TBL1XR1	chr9:3524461-3524896	GM12878	blood:	n/a	n/a
26	MYC	chr9:3524135-3524765	MCF10A-Er-Src	breast:	n/a	chr9:3524737-3524747
27	POLR2A	chr9:3524469-3524924	GM12878	blood:	n/a	n/a
28	IRF1	chr9:3524351-3524886	K562	blood:	n/a	chr9:3524710-3524730 chr9:3524457-3524471 chr9:3524459-3524472 chr9:3524711-3524728 chr9:3524712-3524726 chr9:3524461-3524471 chr9:3524712-3524723
29	ARID3A	chr9:3524387-3524926	K562	blood:	n/a	n/a
30	EP300	chr9:3524433-3524885	GM12878	blood:	n/a	chr9:3524456-3524470
31	POLR2A	chr9:3524452-3525020	GM12878	blood:	n/a	n/a
32	TBP	chr9:3524419-3524847	GM12878	blood:	n/a	n/a
33	POLR2A	chr9:3524494-3524897	GM12891	blood:	n/a	n/a
34	RUNX3	chr9:3524438-3525132	GM12878	blood:	n/a	n/a
35	MXI1	chr9:3524072-3528253	SK-N-SH	brain:	n/a	chr9:3525863-3525878
36	MYC	chr9:3524312-3524913	MCF10A-Er-Src	breast:	n/a	chr9:3524737-3524747
37	POLR2A	chr9:3524416-3524884	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:3501077..3503324-chr9:3523015..3525744,2	MCF-7	breast:
2	chr9:3510896..3512703-chr9:3523478..3525761,2	MCF-7	breast:
3	chr9:3489743..3491847-chr9:3522486..3524735,2	K562	blood:
4	chr10:102106174..102108019-chr9:3523293..3526279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232104	TF binding region
ENSG00000099194	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv539944	chr9:3476471-3535344	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	esv2477708	chr9:3523180-3524864	Active TSS Flanking Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3480600-3524600	Weak transcription	Left Ventricle	heart
2	chr9:3512000-3525000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:3515600-3525000	Weak transcription	Small Intestine	intestine
4	chr9:3517000-3524600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:3520800-3524600	Weak transcription	Lung	lung
6	chr9:3521000-3524600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:3521000-3524800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:3521400-3524600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:3521800-3529000	Active TSS	GM12878-XiMat	blood
10	chr9:3522200-3524600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr9:3522600-3530200	Active TSS	K562	blood
12	chr9:3522800-3527400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:3523000-3526800	Active TSS	NH-A	brain
14	chr9:3523000-3527200	Active TSS	Brain Anterior Caudate	brain
15	chr9:3523200-3524800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:3523200-3525000	Active TSS	Brain Germinal Matrix	brain
17	chr9:3523200-3527000	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr9:3523200-3527200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:3523200-3527200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr9:3523600-3525400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:3523600-3528200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr9:3523600-3528600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:3523800-3524800	Flanking Active TSS	Dnd41	blood
24	chr9:3523800-3525000	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr9:3523800-3526800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:3523800-3527000	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr9:3523800-3527000	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr9:3524000-3524600	Flanking Active TSS	Fetal Brain Female	brain
29	chr9:3524000-3524600	Enhancers	Fetal Heart	heart
30	chr9:3524000-3524600	Weak transcription	HSMM	muscle
31	chr9:3524000-3524800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:3524000-3524800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr9:3524000-3524800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:3524000-3527000	Active TSS	NHLF	lung
35	chr9:3524000-3527200	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr9:3524000-3527200	Active TSS	HMEC	breast
37	chr9:3524000-3527400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:3524000-3527400	Active TSS	NHDF-Ad	bronchial
39	chr9:3524200-3524600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr9:3524200-3524600	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr9:3524200-3524600	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr9:3524200-3524600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr9:3524200-3524800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr9:3524200-3524800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr9:3524200-3525000	Flanking Active TSS	HUVEC	blood vessel
46	chr9:3524200-3525400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:3524200-3525600	Active TSS	Fetal Brain Male	brain
48	chr9:3524200-3526200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr9:3524200-3527000	Active TSS	Primary T cells fromperipheralblood	blood
50	chr9:3524200-3527000	Active TSS	Duodenum Mucosa	Duodenum

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