Variant report

Variant	rs3802455
Chromosome Location	chr9:97780992-97780993
allele	C/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	UBTF	chr9:97780908-97781196	K562	blood:	n/a	n/a
2	SP1	chr9:97780553-97781372	HCT-116	colon:	n/a	n/a
3	TCF12	chr9:97780370-97781693	A549	lung:	n/a	n/a
4	POLR2A	chr9:97780925-97781264	ProgFib	skin:	n/a	n/a
5	POLR2A	chr9:97780929-97781260	A549	lung:	n/a	n/a
6	JUND	chr9:97780511-97781297	A549	lung:	n/a	chr9:97780771-97780780 chr9:97780769-97780780 chr9:97780844-97780852 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780
7	FOS	chr9:97780586-97781203	MCF10A-Er-Src	breast:	n/a	chr9:97780771-97780780 chr9:97780844-97780852 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780769-97780780
8	POLR2A	chr9:97780551-97781389	U87	brain:	n/a	n/a
9	ZBTB33	chr9:97780634-97781260	A549	lung:	n/a	n/a
10	POLR2A	chr9:97780299-97781609	U87	brain:	n/a	n/a
11	CTCF	chr9:97780920-97781070	HPAF	blood vessel:	n/a	n/a
12	FOS	chr9:97780582-97781214	HUVEC	blood vessel:	n/a	chr9:97780771-97780780 chr9:97780844-97780852 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780769-97780780
13	POLR2A	chr9:97780876-97781223	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr9:97780921-97781219	A549	lung:	n/a	n/a
15	STAT3	chr9:97780567-97781086	MCF10A-Er-Src	breast:	n/a	chr9:97780771-97780780
16	ATF3	chr9:97780475-97781163	A549	lung:	n/a	n/a
17	EP300	chr9:97780672-97781050	SK-N-SH_RA	brain:	n/a	chr9:97781013-97781029 chr9:97780770-97780779
18	PBX3	chr9:97780536-97781176	SK-N-SH	brain:	n/a	n/a
19	STAT3	chr9:97780607-97781400	MCF10A-Er-Src	breast:	n/a	chr9:97780771-97780780
20	MAX	chr9:97780868-97781179	K562	blood:	n/a	n/a
21	MAFK	chr9:97780765-97781164	K562	blood:	n/a	n/a
22	GATA3	chr9:97779666-97781556	A549	lung:	n/a	n/a
23	STAT3	chr9:97780301-97781741	MCF10A-Er-Src	breast:	n/a	chr9:97780771-97780780
24	POLR2A	chr9:97780884-97781279	MCF-7	breast:	n/a	n/a
25	ATF1	chr9:97780819-97781197	K562	blood:	n/a	n/a
26	JUN	chr9:97780599-97781049	HUVEC	blood vessel:	n/a	chr9:97780771-97780780 chr9:97780844-97780852 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780
27	CTCF	chr9:97780880-97781030	HPAF	blood vessel:	n/a	n/a
28	MAX	chr9:97780559-97781104	SK-N-SH	brain:	n/a	chr9:97780770-97780779
29	CEBPB	chr9:97780625-97781275	IMR90	lung:	n/a	n/a
30	NR3C1	chr9:97780602-97781107	A549	lung:	n/a	chr9:97780913-97780920 chr9:97780851-97780869 chr9:97780844-97780853
31	TEAD4	chr9:97780410-97781170	SK-N-SH	brain:	n/a	n/a
32	MAX	chr9:97780463-97781598	A549	lung:	n/a	chr9:97780770-97780779
33	NR3C1	chr9:97780638-97781294	A549	lung:	n/a	chr9:97780913-97780920 chr9:97780851-97780869 chr9:97780844-97780853
34	MYC	chr9:97780507-97781388	MCF10A-Er-Src	breast:	n/a	chr9:97780770-97780779
35	MYC	chr9:97780907-97781215	K562	blood:	n/a	n/a
36	REST	chr9:97780834-97781224	A549	lung:	n/a	n/a
37	TCF12	chr9:97780457-97781404	SK-N-SH	brain:	n/a	n/a
38	NR3C1	chr9:97780940-97781196	A549	lung:	n/a	n/a
39	TCF12	chr9:97780574-97781268	A549	lung:	n/a	n/a
40	RCOR1	chr9:97780901-97781206	K562	blood:	n/a	n/a
41	MAX	chr9:97780217-97781187	A549	lung:	n/a	chr9:97780770-97780779
42	MAX	chr9:97779614-97781640	A549	lung:	n/a	chr9:97780770-97780779
43	EP300	chr9:97779856-97781372	A549	lung:	n/a	chr9:97781013-97781029 chr9:97780770-97780779
44	GATA3	chr9:97780457-97781222	SK-N-SH	brain:	n/a	n/a
45	MAX	chr9:97780539-97781290	HCT-116	colon:	n/a	chr9:97780770-97780779
46	MAFK	chr9:97780532-97781364	IMR90	lung:	n/a	n/a
47	CTCF	chr9:97780980-97781130	HBMEC	blood vessel:	n/a	n/a
48	FOSL2	chr9:97779833-97781484	A549	lung:	n/a	chr9:97780771-97780780 chr9:97780844-97780852 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780
49	POLR2A	chr9:97780925-97781236	HepG2	liver:	n/a	n/a
50	FOS	chr9:97779997-97781508	MCF10A-Er-Src	breast:	n/a	chr9:97780771-97780780 chr9:97780844-97780852 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780769-97780780

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:

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

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12684823	0.80[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs4744381	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97768000-97781000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97768000-97781000	Weak transcription	Gastric	stomach
3	chr9:97768000-97783800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr9:97768000-97786200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:97768800-97781800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:97768800-97785600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:97769000-97783800	Weak transcription	Fetal Brain Male	brain
8	chr9:97769000-97787600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:97769600-97784200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:97769600-97790200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr9:97770000-97781200	Weak transcription	Small Intestine	intestine
12	chr9:97770800-97781600	Weak transcription	Colonic Mucosa	Colon
13	chr9:97770800-97782000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:97770800-97782200	Weak transcription	Lung	lung
15	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
16	chr9:97771000-97781600	Weak transcription	Primary B cells from cord blood	blood
17	chr9:97772000-97782200	Weak transcription	Esophagus	oesophagus
18	chr9:97773000-97782200	Weak transcription	Spleen	Spleen
19	chr9:97773200-97793200	Weak transcription	Brain Germinal Matrix	brain
20	chr9:97776000-97781000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr9:97776000-97784400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr9:97776000-97784600	Strong transcription	Placenta	Placenta
23	chr9:97776400-97785400	Strong transcription	Fetal Intestine Large	intestine
24	chr9:97777200-97782200	Weak transcription	Stomach Mucosa	stomach
25	chr9:97777400-97794200	Weak transcription	Thymus	Thymus
26	chr9:97777600-97781000	Weak transcription	Psoas Muscle	Psoas
27	chr9:97778800-97781000	Genic enhancers	Muscle Satellite Cultured Cells	--
28	chr9:97778800-97781000	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr9:97778800-97786200	Genic enhancers	Osteobl	bone
30	chr9:97779000-97782800	Genic enhancers	HSMMtube	muscle
31	chr9:97779200-97781000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:97779200-97782200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:97779200-97782200	Weak transcription	Fetal Intestine Small	intestine
34	chr9:97779200-97782400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr9:97779400-97781200	Genic enhancers	HepG2	liver
36	chr9:97779400-97781800	Enhancers	Brain Substantia Nigra	brain
37	chr9:97779400-97782400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
38	chr9:97779400-97782800	Transcr. at gene 5' and 3'	A549	lung
39	chr9:97779400-97789200	Genic enhancers	Liver	Liver
40	chr9:97779800-97781600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:97779800-97781600	Enhancers	K562	blood
42	chr9:97779800-97782800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:97780000-97781600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:97780000-97781600	Genic enhancers	Duodenum Mucosa	Duodenum
45	chr9:97780000-97781600	Enhancers	HUVEC	blood vessel
46	chr9:97780000-97781600	Transcr. at gene 5' and 3'	NH-A	brain
47	chr9:97780000-97781800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr9:97780000-97782000	Active TSS	Aorta	Aorta
49	chr9:97780000-97782200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr9:97780200-97781000	Enhancers	Brain Inferior Temporal Lobe	brain

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