Variant report

Variant	rs530860165
Chromosome Location	chr9:97766004-97766005
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	STAT3	chr9:97765938-97766303	MCF10A-Er-Src	breast:	n/a	chr9:97766118-97766127 chr9:97766116-97766130 chr9:97766119-97766128
2	SIX5	chr9:97765918-97766734	A549	lung:	n/a	n/a
3	POLR2A	chr9:97765950-97767012	HUVEC	blood vessel:	n/a	n/a
4	SP1	chr9:97765773-97767001	A549	lung:	n/a	chr9:97766690-97766699
5	POLR2A	chr9:97765858-97769286	Hela-S3	cervix:	n/a	n/a
6	RFX5	chr9:97764166-97767012	SK-N-SH	brain:	n/a	chr9:97764370-97764385 chr9:97764370-97764385
7	REST	chr9:97765810-97767007	A549	lung:	n/a	n/a
8	CHD1	chr9:97765419-97769266	IMR90	lung:	n/a	chr9:97766713-97766723 chr9:97767626-97767636
9	EP300	chr9:97765905-97766841	A549	lung:	n/a	chr9:97766680-97766696
10	FOSL2	chr9:97765943-97766921	A549	lung:	n/a	n/a
11	FOXA2	chr9:97765836-97766423	A549	lung:	n/a	chr9:97766157-97766169
12	CEBPB	chr9:97765856-97766450	A549	lung:	n/a	n/a
13	TCF12	chr9:97765754-97767101	A549	lung:	n/a	n/a
14	MAX	chr9:97765914-97768123	A549	lung:	n/a	chr9:97767735-97767745
15	SIN3AK20	chr9:97765999-97766660	A549	lung:	n/a	n/a
16	EP300	chr9:97765574-97766722	A549	lung:	n/a	chr9:97765751-97765760 chr9:97766680-97766696
17	BCL3	chr9:97765727-97767002	A549	lung:	n/a	chr9:97766733-97766746
18	GATA3	chr9:97765788-97768152	A549	lung:	n/a	chr9:97767746-97767757
19	POLR2A	chr9:97765931-97766980	SK-N-SH	brain:	n/a	n/a
20	TCF7L2	chr9:97765926-97766283	HepG2	liver:	n/a	n/a
21	RFX5	chr9:97765894-97767171	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97728899..97731372-chr9:97764520..97766152,2	MCF-7	breast:
2	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
3	chr9:97763979..97769403-chr9:97805439..97812937,10	MCF-7	breast:
4	chr9:97765581..97769970-chr9:97809027..97814302,8	MCF-7	breast:
5	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
6	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000207617	Chromatin interaction
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	esv3393598	chr9:97765956-97768504	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97736600-97766200	Weak transcription	Right Ventricle	heart
2	chr9:97755200-97766400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:97758400-97766400	Weak transcription	Gastric	stomach
4	chr9:97758600-97766400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:97759200-97766200	Weak transcription	Brain Angular Gyrus	brain
6	chr9:97759200-97766200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:97759400-97766200	Weak transcription	Stomach Mucosa	stomach
8	chr9:97762200-97766200	Weak transcription	Placenta	Placenta
9	chr9:97763400-97766400	Weak transcription	Lung	lung
10	chr9:97763600-97766200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:97763600-97766200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr9:97763600-97766200	Weak transcription	Right Atrium	heart
13	chr9:97763600-97766400	Weak transcription	Psoas Muscle	Psoas
14	chr9:97765000-97766200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:97765000-97766200	Enhancers	Brain Hippocampus Middle	brain
16	chr9:97765000-97766200	Enhancers	Fetal Intestine Small	intestine
17	chr9:97765000-97768600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:97765000-97770400	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr9:97765200-97766200	Enhancers	Brain Anterior Caudate	brain
20	chr9:97765200-97766200	Enhancers	Brain Cingulate Gyrus	brain
21	chr9:97765200-97766200	Enhancers	Brain Substantia Nigra	brain
22	chr9:97765200-97770600	Active TSS	Aorta	Aorta
23	chr9:97765400-97766200	Weak transcription	Left Ventricle	heart
24	chr9:97765400-97766400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:97765400-97766400	Weak transcription	Pancreas	Pancrea
26	chr9:97765400-97767800	Active TSS	HSMM	muscle
27	chr9:97765600-97766200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:97765600-97766200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:97765800-97766200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
30	chr9:97765800-97766400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:97765800-97767000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:97765800-97767800	Active TSS	Liver	Liver
33	chr9:97765800-97767800	Active TSS	A549	lung
34	chr9:97765800-97770800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr9:97765800-97772600	Active TSS	Stomach Smooth Muscle	stomach
36	chr9:97766000-97766200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:97766000-97766200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:97766000-97766200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
39	chr9:97766000-97766200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
40	chr9:97766000-97766200	Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr9:97766000-97766200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
42	chr9:97766000-97766200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr9:97766000-97766200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:97766000-97766200	Enhancers	Adipose Nuclei	Adipose
45	chr9:97766000-97766200	Flanking Active TSS	Fetal Kidney	kidney
46	chr9:97766000-97766200	Enhancers	HMEC	breast
47	chr9:97766000-97766200	Enhancers	K562	blood
48	chr9:97766000-97766200	Active TSS	NH-A	brain
49	chr9:97766000-97766400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:97766000-97766400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell

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