Variant report

Variant	rs555964147
Chromosome Location	chr9:96337764-96337765
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	POLR2A	chr9:96337579-96339836	GM18505	blood:	n/a	n/a
2	POLR2A	chr9:96337483-96339925	K562	blood:	n/a	n/a
3	SPI1	chr9:96337638-96338429	GM12878	blood:	n/a	chr9:96338155-96338164 chr9:96338076-96338083 chr9:96338153-96338166 chr9:96338156-96338163 chr9:96338152-96338165 chr9:96338152-96338165
4	REST	chr9:96337337-96340269	H1-neurons	neurons:	n/a	chr9:96339630-96339643 chr9:96339814-96339832 chr9:96338320-96338330
5	POLR2A	chr9:96337533-96339108	IMR90	lung:	n/a	n/a
6	MAZ	chr9:96337511-96340494	IMR90	lung:	n/a	chr9:96339336-96339346 chr9:96339537-96339547 chr9:96338698-96338708 chr9:96340026-96340036
7	POLR2A	chr9:96337591-96337908	ECC-1	luminal epithelium:	n/a	n/a
8	CHD2	chr9:96337690-96338284	GM12878	blood:	n/a	chr9:96337908-96337918
9	MYC	chr9:96337717-96337851	MCF-7	breast:	n/a	n/a
10	POLR2A	chr9:96337742-96337806	Gliobla	brain:	n/a	n/a
11	POLR2A	chr9:96337746-96339956	GM19099	blood:	n/a	n/a
12	SIN3A	chr9:96337438-96339212	H1-hESC	embryonic stem cell:	n/a	chr9:96337571-96337582
13	POLR2A	chr9:96337303-96339398	ProgFib	skin:	n/a	n/a
14	POLR2A	chr9:96337546-96339247	MCF-7	breast:	n/a	n/a
15	ZNF263	chr9:96337395-96338327	HEK293-T-REx	kidney:	n/a	chr9:96337852-96337861 chr9:96338214-96338223 chr9:96337725-96337734 chr9:96337696-96337717
16	ZBTB7A	chr9:96337705-96338819	ECC-1	luminal epithelium:	n/a	chr9:96338482-96338490 chr9:96337913-96337920
17	POLR2A	chr9:96337595-96339308	MCF-7	breast:	n/a	n/a
18	POLR2A	chr9:96337521-96339325	K562	blood:	n/a	n/a
19	POLR2A	chr9:96337513-96339534	MCF-7	breast:	n/a	n/a
20	POLR2A	chr9:96337491-96338819	GM12878	blood:	n/a	n/a
21	ELF1	chr9:96337620-96338744	GM12878	blood:	n/a	chr9:96338152-96338165 chr9:96338153-96338164
22	POLR2A	chr9:96337692-96337874	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr9:96337679-96339934	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr9:96337703-96338834	PBDE	blood:	n/a	n/a
25	POLR2A	chr9:96337705-96340169	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr9:96337575-96339807	GM12892	blood:	n/a	n/a
27	SMARCB1	chr9:96337503-96338799	Hela-S3	cervix:	n/a	n/a
28	CTBP2	chr9:96337422-96338326	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:96211528..96214948-chr9:96337573..96343441,10	MCF-7	breast:
2	chr9:96211672..96218862-chr9:96335264..96341672,16	MCF-7	breast:
3	chr9:96337024..96339848-chr9:96617971..96619932,2	MCF-7	breast:
4	chr9:95856094..95858375-chr9:96337008..96340445,3	MCF-7	breast:
5	chr9:96337657..96339290-chr9:96927321..96930180,2	K562	blood:

Variant related genes	Relation type
PHF2	TF binding region
ENSG00000269946	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000223446	Chromatin interaction
ENSG00000231990	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041803	chr9:96299639-96342013	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv824985	chr9:96337735-96340349	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96336600-96337800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
2	chr9:96336600-96337800	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr9:96336600-96337800	Enhancers	Spleen	Spleen
4	chr9:96336800-96337800	Enhancers	Primary B cells from peripheral blood	blood
5	chr9:96336800-96337800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr9:96336800-96338000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:96337000-96337800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr9:96337000-96338200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:96337000-96338400	Enhancers	Fetal Heart	heart
10	chr9:96337200-96337800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:96337200-96337800	Flanking Active TSS	Colon Smooth Muscle	Colon
12	chr9:96337200-96337800	Flanking Active TSS	NHDF-Ad	bronchial
13	chr9:96337200-96337800	Flanking Active TSS	Osteobl	bone
14	chr9:96337200-96338000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:96337200-96338000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:96337200-96338000	Enhancers	Fetal Brain Male	brain
17	chr9:96337200-96338000	Flanking Active TSS	Rectal Smooth Muscle	rectum
18	chr9:96337200-96338000	Flanking Active TSS	HepG2	liver
19	chr9:96337200-96338200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:96337200-96338200	Flanking Active TSS	Placenta	Placenta
21	chr9:96337200-96338200	Flanking Active TSS	Dnd41	blood
22	chr9:96337200-96338400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:96337200-96338400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:96337200-96338400	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr9:96337400-96337800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr9:96337400-96337800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr9:96337400-96337800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
28	chr9:96337400-96337800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:96337400-96337800	Enhancers	Primary B cells from cord blood	blood
30	chr9:96337400-96337800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:96337400-96337800	Enhancers	Liver	Liver
32	chr9:96337400-96337800	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr9:96337400-96337800	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr9:96337400-96337800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr9:96337400-96337800	Flanking Active TSS	HSMM	muscle
36	chr9:96337400-96337800	Enhancers	K562	blood
37	chr9:96337400-96338000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
38	chr9:96337400-96338000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:96337400-96338000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:96337400-96338000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:96337400-96338000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr9:96337400-96338000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:96337400-96338000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr9:96337400-96338000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:96337400-96338000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr9:96337400-96338000	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr9:96337400-96338000	Flanking Active TSS	Colonic Mucosa	Colon
48	chr9:96337400-96338000	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr9:96337400-96338000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr9:96337400-96338000	Flanking Active TSS	Fetal Intestine Large	intestine

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