Variant report

Variant	rs143357963
Chromosome Location	chr9:3523956-3523957
allele	A/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	POLR2A	chr9:3520146-3530139	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr9:3523842-3524121	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr9:3523584-3529804	MCF10A-Er-Src	breast:	n/a	n/a
4	CHD1	chr9:3523733-3524024	GM12878	blood:	n/a	n/a
5	IRF1	chr9:3523747-3524078	K562	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:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3474400-3524400	Weak transcription	Thymus	Thymus
2	chr9:3480600-3524600	Weak transcription	Left Ventricle	heart
3	chr9:3503000-3524400	Weak transcription	Fetal Thymus	thymus
4	chr9:3509000-3524400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:3512000-3524200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:3512000-3524400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:3512000-3525000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:3513800-3524400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr9:3515600-3525000	Weak transcription	Small Intestine	intestine
10	chr9:3517000-3524600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:3517800-3524000	Weak transcription	NHDF-Ad	bronchial
12	chr9:3518000-3524400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr9:3518200-3524400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:3519400-3524400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr9:3520800-3524400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:3520800-3524400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:3520800-3524600	Weak transcription	Lung	lung
18	chr9:3521000-3524000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:3521000-3524400	Weak transcription	Fetal Kidney	kidney
20	chr9:3521000-3524600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:3521000-3524800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:3521400-3524600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:3521800-3524000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr9:3521800-3524200	Enhancers	Primary T cells from cord blood	blood
25	chr9:3521800-3529000	Active TSS	GM12878-XiMat	blood
26	chr9:3522000-3524200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr9:3522000-3524200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr9:3522000-3524200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr9:3522200-3524000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr9:3522200-3524200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr9:3522200-3524400	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr9:3522200-3524600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr9:3522400-3524400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:3522600-3524000	Weak transcription	HepG2	liver
35	chr9:3522600-3530200	Active TSS	K562	blood
36	chr9:3522800-3524000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:3522800-3524000	Enhancers	A549	lung
38	chr9:3522800-3527400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:3523000-3526800	Active TSS	NH-A	brain
40	chr9:3523000-3527200	Active TSS	Brain Anterior Caudate	brain
41	chr9:3523200-3524000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:3523200-3524000	Weak transcription	Brain Angular Gyrus	brain
43	chr9:3523200-3524000	Weak transcription	Hela-S3	cervix
44	chr9:3523200-3524200	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr9:3523200-3524200	Weak transcription	Brain Hippocampus Middle	brain
46	chr9:3523200-3524400	Enhancers	Colon Smooth Muscle	Colon
47	chr9:3523200-3524800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:3523200-3525000	Active TSS	Brain Germinal Matrix	brain
49	chr9:3523200-3527000	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr9:3523200-3527200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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