Variant report

Variant	rs55863440
Chromosome Location	chr15:40544617-40544618
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	TCF12	chr15:40544458-40545562	ECC-1	luminal epithelium:	n/a	n/a
2	SIN3A	chr15:40544271-40545134	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr15:40544451-40545629	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr15:40544595-40545462	ECC-1	luminal epithelium:	n/a	n/a
5	ZBTB7A	chr15:40544361-40545697	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr15:40544611-40545649	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr15:40544388-40545608	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr15:40544153-40545616	H1-hESC	embryonic stem cell:	n/a	n/a
9	GABPA	chr15:40544393-40545479	H1-hESC	embryonic stem cell:	n/a	chr15:40545274-40545283
10	POLR2A	chr15:40544478-40545591	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr15:40544447-40545613	ECC-1	luminal epithelium:	n/a	n/a
12	MAX	chr15:40544422-40545678	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr15:40544442-40545493	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr15:40544520-40545424	HCT-116	colon:	n/a	n/a
15	GABPA	chr15:40544343-40545626	H1-hESC	embryonic stem cell:	n/a	chr15:40545274-40545283
16	E2F6	chr15:40544008-40545766	H1-hESC	embryonic stem cell:	n/a	chr15:40544806-40544821 chr15:40544808-40544820 chr15:40545274-40545283 chr15:40544806-40544821
17	MAX	chr15:40544517-40545017	MCF-7	breast:	n/a	n/a
18	TBP	chr15:40544459-40544904	H1-hESC	embryonic stem cell:	n/a	n/a
19	USF1	chr15:40544476-40544987	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr15:40544180-40545383	H1-hESC	embryonic stem cell:	n/a	n/a
21	USF1	chr15:40544569-40544985	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr15:40544579-40545343	HCT-116	colon:	n/a	n/a
23	TEAD4	chr15:40544533-40545065	ECC-1	luminal epithelium:	n/a	n/a
24	MAX	chr15:40544432-40544892	H1-hESC	embryonic stem cell:	n/a	n/a
25	E2F6	chr15:40544278-40545624	H1-hESC	embryonic stem cell:	n/a	chr15:40544806-40544821 chr15:40544808-40544820 chr15:40545274-40545283 chr15:40544806-40544821
26	ZBTB7A	chr15:40544165-40545355	ECC-1	luminal epithelium:	n/a	n/a
27	EP300	chr15:40544459-40545592	ECC-1	luminal epithelium:	n/a	chr15:40545274-40545283 chr15:40544826-40544842

Variant related genes	Relation type
PAK6	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1048163	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048164	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11634057	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634409	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636097	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638662	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638733	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050520	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55799438	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55974545	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731469	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731470	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900054	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv904095	chr15:40525430-40591570	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv471240	chr15:40528155-40595627	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40542400-40544800	Weak transcription	Brain Angular Gyrus	brain
2	chr15:40542600-40544800	Weak transcription	Gastric	stomach
3	chr15:40542800-40545200	Weak transcription	HMEC	breast
4	chr15:40543200-40546200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:40543400-40544800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr15:40544000-40544800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:40544000-40544800	Enhancers	Left Ventricle	heart
8	chr15:40544000-40546000	Bivalent Enhancer	Fetal Brain Male	brain
9	chr15:40544200-40544800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:40544200-40544800	Enhancers	Lung	lung
11	chr15:40544200-40544800	Flanking Active TSS	Pancreas	Pancrea
12	chr15:40544200-40544800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr15:40544200-40544800	Bivalent Enhancer	Spleen	Spleen
14	chr15:40544200-40545200	Weak transcription	Fetal Heart	heart
15	chr15:40544200-40545400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr15:40544200-40545400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:40544200-40545400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:40544200-40545600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr15:40544200-40545600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:40544200-40545800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
21	chr15:40544200-40545800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr15:40544400-40544800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:40544400-40544800	Weak transcription	Brain Substantia Nigra	brain
24	chr15:40544400-40544800	Bivalent Enhancer	Fetal Thymus	thymus
25	chr15:40544400-40544800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
26	chr15:40544400-40544800	Enhancers	Small Intestine	intestine
27	chr15:40544400-40545000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
28	chr15:40544400-40545200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:40544400-40545200	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr15:40544400-40545400	Active TSS	Duodenum Mucosa	Duodenum
31	chr15:40544400-40545400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
32	chr15:40544400-40545600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:40544400-40545800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr15:40544400-40545800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr15:40544400-40545800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:40544400-40545800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:40544400-40545800	Flanking Active TSS	Esophagus	oesophagus
38	chr15:40544400-40545800	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr15:40544600-40544800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:40544600-40544800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:40544600-40544800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr15:40544600-40544800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
43	chr15:40544600-40544800	Bivalent Enhancer	Primary B cells from cord blood	blood
44	chr15:40544600-40544800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
45	chr15:40544600-40544800	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
46	chr15:40544600-40544800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:40544600-40544800	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:40544600-40544800	Bivalent/Poised TSS	Fetal Brain Female	brain
49	chr15:40544600-40544800	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr15:40544600-40544800	Active TSS	Psoas Muscle	Psoas

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