Variant report

Variant	rs149921064
Chromosome Location	chr5:40679035-40679036
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	GTF2F1	chr5:40678805-40680138	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:40678901-40680830	H1-neurons	neurons:	n/a	n/a
3	CEBPB	chr5:40678612-40679131	MCF-7	breast:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
4	POLR2A	chr5:40678961-40679833	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr5:40678244-40680457	NB4	blood:	n/a	n/a
6	TCF12	chr5:40678786-40679832	A549	lung:	n/a	chr5:40679806-40679813
7	MAX	chr5:40678144-40680687	NB4	blood:	n/a	n/a
8	RAD21	chr5:40678153-40679736	Hela-S3	cervix:	n/a	chr5:40679296-40679306 chr5:40679294-40679306
9	TAF1	chr5:40678937-40680275	A549	lung:	n/a	n/a
10	EBF1	chr5:40678996-40679760	GM12878	blood:	n/a	n/a
11	CEBPB	chr5:40678184-40680090	Hela-S3	cervix:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
12	TBP	chr5:40678152-40680190	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr5:40678512-40680410	U87	brain:	n/a	n/a
14	POLR2A	chr5:40679015-40680302	A549	lung:	n/a	n/a
15	REST	chr5:40679016-40680444	HL-60	blood:	n/a	chr5:40679637-40679650 chr5:40679808-40679821
16	POLR2A	chr5:40678947-40680277	ECC-1	luminal epithelium:	n/a	n/a
17	MXI1	chr5:40678177-40680144	Hela-S3	cervix:	n/a	n/a
18	SIN3A	chr5:40679009-40679787	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF217	chr5:40678929-40679371	MCF-7	breast:	n/a	n/a
20	TAF7	chr5:40679008-40679475	H1-hESC	embryonic stem cell:	n/a	n/a
21	CHD2	chr5:40678769-40680438	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr5:40678555-40679069	A549	lung:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
23	TFAP2C	chr5:40679017-40680425	Hela-S3	cervix:	n/a	n/a
24	SP1	chr5:40678898-40680154	A549	lung:	n/a	chr5:40679922-40679931 chr5:40679920-40679932 chr5:40679939-40679960 chr5:40679921-40679935 chr5:40679920-40679932 chr5:40679921-40679930
25	CEBPB	chr5:40678667-40679358	A549	lung:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
26	POLR2A	chr5:40678949-40680237	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr5:40678546-40680369	PANC-1	pancreas:	n/a	n/a
28	SRF	chr5:40678953-40680216	MCF-7	breast:	n/a	chr5:40679423-40679441 chr5:40679427-40679438 chr5:40679426-40679441 chr5:40679421-40679438 chr5:40679427-40679441 chr5:40679423-40679437
29	RFX5	chr5:40678219-40680202	Hela-S3	cervix:	n/a	n/a
30	SIN3AK20	chr5:40679008-40679450	PANC-1	pancreas:	n/a	n/a
31	E2F4	chr5:40678789-40680148	MCF10A-Er-Src	breast:	n/a	chr5:40679536-40679545
32	ZKSCAN1	chr5:40678910-40680342	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr5:40678997-40680264	IMR90	lung:	n/a	n/a
34	POLR2A	chr5:40679004-40680208	HCT-116	colon:	n/a	n/a
35	MAX	chr5:40678934-40680545	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr5:40678798-40680512	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr5:40678843-40680600	A549	lung:	n/a	n/a
38	USF2	chr5:40678625-40679641	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr5:40678596-40680801	HL-60	blood:	n/a	n/a
40	TAF1	chr5:40679026-40679460	H1-hESC	embryonic stem cell:	n/a	n/a
41	CEBPB	chr5:40678652-40679420	IMR90	lung:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
42	SMARCC1	chr5:40678796-40680595	Hela-S3	cervix:	n/a	n/a
43	TAF1	chr5:40678813-40679548	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr5:40678674-40680297	Hela-S3	cervix:	n/a	n/a
45	BCL3	chr5:40678908-40679451	A549	lung:	n/a	n/a
46	STAT3	chr5:40678190-40679418	Hela-S3	cervix:	n/a	chr5:40678336-40678347 chr5:40678826-40678840 chr5:40678828-40678837 chr5:40678827-40678838 chr5:40679028-40679042 chr5:40678829-40678838 chr5:40678832-40678840 chr5:40678844-40678852
47	E2F6	chr5:40678968-40682262	H1-hESC	embryonic stem cell:	n/a	chr5:40679536-40679545
48	POLR2A	chr5:40678966-40680193	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr5:40678746-40680275	U87	brain:	n/a	n/a
50	POLR2A	chr5:40677912-40680908	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:40678741..40679756-chr6:26123548..26124204,3	Hela-S3	cervix:
2	chr14:94547017..94547649-chr5:40678640..40679465,2	Hela-S3	cervix:
3	chr1:155023041..155023664-chr5:40678966..40679570,2	Hela-S3	cervix:
4	chr17:43224484..43225221-chr5:40678825..40679523,2	NB4	blood:
5	chr15:65321890..65322402-chr5:40678654..40679608,2	NB4	blood:
6	chr1:36235070..36236025-chr5:40679016..40679937,2	Hela-S3	cervix:
7	chr5:40678654..40679643-chr5:89705625..89706304,2	NB4	blood:
8	chr15:31619156..31619701-chr5:40678819..40679598,2	Hela-S3	cervix:
9	chr20:62259613..62260132-chr5:40679006..40679597,2	Hela-S3	cervix:
10	chr5:40673402..40675876-chr5:40676322..40679263,4	K562	blood:
11	chr5:40505949..40508818-chr5:40677222..40679235,2	MCF-7	breast:
12	chr11:62608481..62609314-chr5:40678890..40679963,4	Hela-S3	cervix:
13	chr5:40677072..40679518-chr5:40680792..40683406,4	MCF-7	breast:
14	chr14:75745262..75745853-chr5:40678732..40679322,2	Hela-S3	cervix:
15	chr1:242011208..242011713-chr5:40678933..40679886,2	Hela-S3	cervix:
16	chr2:204103696..204104264-chr5:40678600..40679556,2	Hela-S3	cervix:

Variant related genes	Relation type
PTGER4	TF binding region
ENSG00000119004	Chromatin interaction
ENSG00000186834	Chromatin interaction
ENSG00000165948	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000174371	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000089737	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000171522	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000103707	Chromatin interaction
ENSG00000092853	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	nsv880993	chr5:40521648-40682550	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
2	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3397684	chr5:40678645-40681143	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40676800-40679200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:40676800-40679200	Flanking Active TSS	HUVEC	blood vessel
3	chr5:40677400-40680800	Active TSS	Duodenum Mucosa	Duodenum
4	chr5:40677400-40681000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr5:40677600-40679200	Weak transcription	Small Intestine	intestine
6	chr5:40677600-40679400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr5:40677800-40679400	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr5:40677800-40680200	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr5:40677800-40681000	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr5:40678000-40679400	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr5:40678200-40679200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr5:40678200-40679400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:40678200-40679400	Bivalent/Poised TSS	Fetal Kidney	kidney
14	chr5:40678200-40680400	Active TSS	Stomach Smooth Muscle	stomach
15	chr5:40678200-40680800	Active TSS	Dnd41	blood
16	chr5:40678400-40679200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr5:40678400-40679400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr5:40678400-40679400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr5:40678400-40680800	Active TSS	A549	lung
20	chr5:40678400-40681000	Active TSS	Fetal Intestine Small	intestine
21	chr5:40678400-40681000	Active TSS	Thymus	Thymus
22	chr5:40678400-40681400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:40678400-40682000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:40678400-40683800	Active TSS	HSMM	muscle
25	chr5:40678400-40684600	Active TSS	HSMMtube	muscle
26	chr5:40678600-40679200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
27	chr5:40678600-40679200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:40678600-40679200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr5:40678600-40679200	Flanking Active TSS	NH-A	brain
30	chr5:40678600-40679200	Flanking Active TSS	Osteobl	bone
31	chr5:40678600-40679400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr5:40678600-40679400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr5:40678600-40679400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:40678600-40679400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr5:40678600-40679400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr5:40678600-40680000	Active TSS	H1 Cell Line	embryonic stem cell
37	chr5:40678600-40680400	Active TSS	Colonic Mucosa	Colon
38	chr5:40678600-40680400	Active TSS	Right Ventricle	heart
39	chr5:40678600-40680600	Active TSS	Stomach Mucosa	stomach
40	chr5:40678600-40680800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr5:40678600-40681000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:40678600-40681200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:40678600-40681200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:40678600-40681200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:40678600-40682200	Active TSS	NHEK	skin
46	chr5:40678600-40684400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr5:40678600-40685800	Active TSS	Right Atrium	heart
48	chr5:40678800-40679200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:40678800-40679200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr5:40678800-40679200	Active TSS	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links