Variant report

Variant	rs560772279
Chromosome Location	chr5:154134420-154134421
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	CEBPB	chr5:154134299-154134943	A549	lung:	n/a	n/a
2	YY1	chr5:154134135-154135991	ECC-1	luminal epithelium:	n/a	chr5:154135832-154135846 chr5:154134391-154134400 chr5:154135945-154135959
3	WRNIP1	chr5:154133876-154134738	GM12878	blood:	n/a	n/a
4	RAD21	chr5:154134324-154134908	MCF-7	breast:	n/a	n/a
5	YY1	chr5:154134172-154134769	K562	blood:	n/a	chr5:154134391-154134400
6	EP300	chr5:154134335-154134864	T-47D	breast:	n/a	chr5:154134558-154134574 chr5:154134391-154134400
7	E2F6	chr5:154134120-154134939	Hela-S3	cervix:	n/a	chr5:154134136-154134145 chr5:154134202-154134212
8	TCF12	chr5:154133420-154136643	A549	lung:	n/a	chr5:154133494-154133502 chr5:154134317-154134324
9	CREB1	chr5:154134255-154135097	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYC	chr5:154133822-154136192	K562	blood:	n/a	chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154134650-154134659 chr5:154134657-154134668 chr5:154134658-154134667
11	PAX5	chr5:154134151-154134911	GM12892	blood:	n/a	n/a
12	ZKSCAN1	chr5:154134214-154134770	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr5:154133997-154135429	PANC-1	pancreas:	n/a	n/a
14	TCF12	chr5:154134183-154135580	ECC-1	luminal epithelium:	n/a	chr5:154134317-154134324
15	CEBPD	chr5:154134379-154134814	K562	blood:	n/a	n/a
16	PBX3	chr5:154134327-154135690	A549	lung:	n/a	n/a
17	SIN3AK20	chr5:154134213-154137170	PANC-1	pancreas:	n/a	n/a
18	EGR1	chr5:154134382-154135434	K562	blood:	n/a	chr5:154134388-154134398 chr5:154135301-154135311 chr5:154135262-154135276 chr5:154134666-154134679 chr5:154134667-154134676 chr5:154134389-154134399 chr5:154134385-154134400 chr5:154134386-154134399 chr5:154135261-154135274 chr5:154134386-154134399
19	E2F4	chr5:154134117-154135572	K562	blood:	n/a	chr5:154134136-154134145 chr5:154134202-154134212 chr5:154135302-154135311
20	GTF2F1	chr5:154134075-154134732	K562	blood:	n/a	n/a
21	RCOR1	chr5:154134389-154134863	HepG2	liver:	n/a	n/a
22	POLR2A	chr5:154133143-154136943	K562	blood:	n/a	n/a
23	SIN3A	chr5:154134089-154134760	GM12878	blood:	n/a	chr5:154134277-154134290
24	TCF12	chr5:154134362-154134760	H1-hESC	embryonic stem cell:	n/a	n/a
25	REST	chr5:154134136-154134719	A549	lung:	n/a	chr5:154134277-154134290 chr5:154134592-154134605
26	EP300	chr5:154134278-154134765	H1-hESC	embryonic stem cell:	n/a	chr5:154134558-154134574 chr5:154134283-154134299 chr5:154134391-154134400
27	BCLAF1	chr5:154134300-154134925	K562	blood:	n/a	n/a
28	UBTF	chr5:154134102-154136984	K562	blood:	n/a	n/a
29	TAF1	chr5:154134058-154135376	H1-hESC	embryonic stem cell:	n/a	n/a
30	EP300	chr5:154134396-154134793	GM12878	blood:	n/a	chr5:154134558-154134574
31	ZNF143	chr5:154134198-154134917	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr5:154134403-154134772	H1-hESC	embryonic stem cell:	n/a	chr5:154134548-154134561
33	POLR2A	chr5:154134056-154135301	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:154133745-154137338	PANC-1	pancreas:	n/a	n/a
35	MYC	chr5:154134079-154136080	Hela-S3	cervix:	n/a	chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154134650-154134659 chr5:154134657-154134668 chr5:154134658-154134667
36	TEAD4	chr5:154134273-154134989	ECC-1	luminal epithelium:	n/a	n/a
37	TAF1	chr5:154134417-154135771	HepG2	liver:	n/a	n/a
38	MAX	chr5:154133989-154135108	H1-hESC	embryonic stem cell:	n/a	chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154134650-154134659 chr5:154134657-154134668 chr5:154134658-154134667
39	TCF3	chr5:154134346-154134812	GM12878	blood:	n/a	n/a
40	CEBPB	chr5:154134379-154134814	H1-hESC	embryonic stem cell:	n/a	n/a
41	NFIC	chr5:154134366-154134745	HepG2	liver:	n/a	n/a
42	KAP1	chr5:154133069-154134713	HEK293	kidney:	n/a	chr5:154134604-154134612
43	BHLHE40	chr5:154133828-154135379	GM12878	blood:	n/a	chr5:154134276-154134292 chr5:154134658-154134667 chr5:154134658-154134667 chr5:154134657-154134666
44	EGR1	chr5:154134382-154134838	H1-hESC	embryonic stem cell:	n/a	chr5:154134388-154134398 chr5:154134666-154134679 chr5:154134667-154134676 chr5:154134389-154134399 chr5:154134385-154134400 chr5:154134386-154134399 chr5:154134386-154134399
45	MAZ	chr5:154134036-154137243	GM12878	blood:	n/a	chr5:154136511-154136521 chr5:154134523-154134532 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154136963-154136973 chr5:154134650-154134659 chr5:154136730-154136740 chr5:154134657-154134668 chr5:154134658-154134667
46	YY1	chr5:154134195-154136130	K562	blood:	n/a	chr5:154135832-154135846 chr5:154134391-154134400 chr5:154135945-154135959
47	CUX1	chr5:154134322-154134515	K562	blood:	n/a	n/a
48	PML	chr5:154134395-154134706	GM12878	blood:	n/a	chr5:154134604-154134612
49	HMGN3	chr5:154134186-154136077	K562	blood:	n/a	n/a
50	POLR2A	chr5:154133986-154134726	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:154114978..154117402-chr5:154132990..154134533,2	MCF-7	breast:
2	chr1:149857405..149859778-chr5:154134028..154135572,2	MCF-7	breast:
3	chr5:154059571..154067369-chr5:154132796..154138140,13	K562	blood:
4	chr1:161369209..161370167-chr5:154134118..154134820,2	Hela-S3	cervix:
5	chr5:154091014..154094062-chr5:154133007..154138054,7	MCF-7	breast:
6	chr19:34286193..34287142-chr5:154134023..154134959,2	Hela-S3	cervix:
7	chr5:154134100..154134844-chr7:112758082..112758656,2	Hela-S3	cervix:
8	chr2:241937634..241938153-chr5:154134116..154135051,2	MCF-7	breast:
9	chr5:154090008..154095548-chr5:154132332..154137735,10	MCF-7	breast:
10	chr5:154133833..154138436-chr5:154316104..154319386,7	K562	blood:
11	chr5:154106800..154109528-chr5:154133013..154134653,2	K562	blood:
12	chr5:154133318..154137368-chr5:154208082..154212477,8	MCF-7	breast:
13	chr5:154059219..154066449-chr5:154131053..154139153,28	MCF-7	breast:
14	chr5:154133591..154135701-chr5:179497285..179498805,3	MCF-7	breast:
15	chr5:154079413..154083903-chr5:154131964..154138437,9	MCF-7	breast:
16	chr11:118955268..118955808-chr5:154134105..154134835,2	HCT-116	colon:
17	chr5:154133224..154141155-chr5:154235246..154242227,24	MCF-7	breast:
18	chr5:154054874..154057570-chr5:154132622..154134440,2	MCF-7	breast:
19	chr5:154122459..154125303-chr5:154131772..154134458,2	MCF-7	breast:
20	chr17:59475759..59478103-chr5:154134019..154136422,2	MCF-7	breast:
21	chr5:154120997..154122721-chr5:154132198..154134766,2	K562	blood:
22	chr5:154108106..154110806-chr5:154133073..154135320,2	K562	blood:
23	chr5:154133665..154137234-chr5:154235811..154241105,6	MCF-7	breast:
24	chr5:154133563..154137747-chr5:154235219..154239187,9	K562	blood:
25	chr5:154134362..154135956-chr5:179498285..179499281,4	HCT-116	colon:
26	chr5:154133441..154135046-chr5:154198681..154200668,2	MCF-7	breast:
27	chr5:154107670..154109549-chr5:154132494..154135385,2	MCF-7	breast:
28	chr5:154133598..154138734-chr5:154235660..154239806,12	K562	blood:
29	chr5:154133384..154135677-chr5:154316370..154317979,2	MCF-7	breast:
30	chr5:154133984..154137613-chr5:154316996..154320177,4	K562	blood:
31	chr17:39844723..39845400-chr5:154133976..154134932,2	Hela-S3	cervix:
32	chr5:154133720..154135863-chr5:154214585..154216471,2	K562	blood:
33	chr2:241938134..241939654-chr5:154133580..154135809,2	K562	blood:

Variant related genes	Relation type
LARP1	TF binding region
ENSG00000153885	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000155508	Chromatin interaction
ENSG00000170271	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000263478	Chromatin interaction
ENSG00000214194	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000162804	Chromatin interaction
ENSG00000263361	Chromatin interaction
ENSG00000256269	Chromatin interaction
ENSG00000082516	Chromatin interaction
ENSG00000221552	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000241187	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021153	chr5:154099869-154147970	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	esv3406300	chr5:154133209-154138557	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	esv3442367	chr5:154133259-154137657	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
4	esv3371359	chr5:154133784-154136632	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
5	esv3375024	chr5:154134009-154135957	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154132600-154134600	Enhancers	Fetal Heart	heart
2	chr5:154133000-154134600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr5:154133000-154134600	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr5:154133200-154134600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr5:154133200-154134600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
6	chr5:154133200-154134600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr5:154133200-154134600	Flanking Active TSS	NH-A	brain
8	chr5:154133200-154134600	Flanking Active TSS	NHLF	lung
9	chr5:154133400-154134600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:154133400-154134600	Flanking Active TSS	HSMM	muscle
11	chr5:154133400-154137200	Active TSS	Lung	lung
12	chr5:154133600-154134600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr5:154133600-154134600	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr5:154133600-154134600	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr5:154133600-154134600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr5:154133600-154134600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:154133600-154134600	Flanking Active TSS	HMEC	breast
18	chr5:154133600-154135800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:154133600-154137600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr5:154133800-154134600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:154133800-154134600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr5:154133800-154134600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr5:154133800-154134600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr5:154133800-154134600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:154133800-154134600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr5:154133800-154134600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:154133800-154134600	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr5:154133800-154134600	Flanking Active TSS	Colonic Mucosa	Colon
29	chr5:154133800-154134600	Flanking Active TSS	Fetal Muscle Trunk	muscle
30	chr5:154133800-154134600	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr5:154133800-154134600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr5:154133800-154134600	Flanking Active TSS	Osteobl	bone
33	chr5:154133800-154135600	Active TSS	Brain Germinal Matrix	brain
34	chr5:154133800-154137200	Active TSS	Esophagus	oesophagus
35	chr5:154133800-154137600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:154133800-154137600	Active TSS	Psoas Muscle	Psoas
37	chr5:154134000-154134600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr5:154134000-154134600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr5:154134000-154134600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr5:154134000-154134600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:154134000-154134600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr5:154134000-154134600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:154134000-154134600	Flanking Active TSS	Liver	Liver
44	chr5:154134000-154134600	Flanking Active TSS	Placenta	Placenta
45	chr5:154134000-154134600	Flanking Active TSS	Pancreas	Pancrea
46	chr5:154134000-154135000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:154134000-154137600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:154134000-154137600	Active TSS	H9 Cell Line	embryonic stem cell
49	chr5:154134000-154137600	Active TSS	Aorta	Aorta
50	chr5:154134000-154137600	Active TSS	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links