Variant report

Variant	rs55974545
Chromosome Location	chr15:40544520-40544521
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	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	ZBTB7A	chr15:40544361-40545697	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr15:40544388-40545608	ECC-1	luminal epithelium:	n/a	n/a
6	MAX	chr15:40544153-40545616	H1-hESC	embryonic stem cell:	n/a	n/a
7	GABPA	chr15:40544393-40545479	H1-hESC	embryonic stem cell:	n/a	chr15:40545274-40545283
8	POLR2A	chr15:40544478-40545591	ECC-1	luminal epithelium:	n/a	n/a
9	NFIC	chr15:40544447-40545613	ECC-1	luminal epithelium:	n/a	n/a
10	MAX	chr15:40544422-40545678	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr15:40544442-40545493	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr15:40544520-40545424	HCT-116	colon:	n/a	n/a
13	GABPA	chr15:40544343-40545626	H1-hESC	embryonic stem cell:	n/a	chr15:40545274-40545283
14	E2F6	chr15:40544008-40545766	H1-hESC	embryonic stem cell:	n/a	chr15:40544806-40544821 chr15:40544808-40544820 chr15:40545274-40545283 chr15:40544806-40544821
15	MAX	chr15:40544517-40545017	MCF-7	breast:	n/a	n/a
16	TBP	chr15:40544459-40544904	H1-hESC	embryonic stem cell:	n/a	n/a
17	USF1	chr15:40544476-40544987	ECC-1	luminal epithelium:	n/a	n/a
18	MYC	chr15:40544268-40544543	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr15:40544180-40545383	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr15:40544432-40544892	H1-hESC	embryonic stem cell:	n/a	n/a
21	E2F6	chr15:40544278-40545624	H1-hESC	embryonic stem cell:	n/a	chr15:40544806-40544821 chr15:40544808-40544820 chr15:40545274-40545283 chr15:40544806-40544821
22	ZBTB7A	chr15:40544165-40545355	ECC-1	luminal epithelium:	n/a	n/a
23	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	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048164	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11634057	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634409	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636097	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638662	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638733	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050520	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55799438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55863440	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731469	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731470	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900054	1.00[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:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40542200-40544600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
2	chr15:40542400-40544600	Weak transcription	Brain Anterior Caudate	brain
3	chr15:40542400-40544800	Weak transcription	Brain Angular Gyrus	brain
4	chr15:40542600-40544800	Weak transcription	Gastric	stomach
5	chr15:40542800-40545200	Weak transcription	HMEC	breast
6	chr15:40543200-40546200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:40543400-40544600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
8	chr15:40543400-40544600	Enhancers	Right Ventricle	heart
9	chr15:40543400-40544800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr15:40543800-40544600	Enhancers	Adipose Nuclei	Adipose
11	chr15:40543800-40544600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:40543800-40544600	Enhancers	Placenta	Placenta
13	chr15:40544000-40544600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:40544000-40544600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr15:40544000-40544600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:40544000-40544600	Enhancers	Brain Hippocampus Middle	brain
17	chr15:40544000-40544600	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr15:40544000-40544800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:40544000-40544800	Enhancers	Left Ventricle	heart
20	chr15:40544000-40546000	Bivalent Enhancer	Fetal Brain Male	brain
21	chr15:40544200-40544600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
22	chr15:40544200-40544600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
23	chr15:40544200-40544600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:40544200-40544600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
25	chr15:40544200-40544600	Bivalent Enhancer	Fetal Stomach	stomach
26	chr15:40544200-40544600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr15:40544200-40544600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
28	chr15:40544200-40544600	Enhancers	Right Atrium	heart
29	chr15:40544200-40544600	Bivalent Enhancer	Stomach Mucosa	stomach
30	chr15:40544200-40544600	Enhancers	Stomach Smooth Muscle	stomach
31	chr15:40544200-40544800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:40544200-40544800	Enhancers	Lung	lung
33	chr15:40544200-40544800	Flanking Active TSS	Pancreas	Pancrea
34	chr15:40544200-40544800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr15:40544200-40544800	Bivalent Enhancer	Spleen	Spleen
36	chr15:40544200-40545200	Weak transcription	Fetal Heart	heart
37	chr15:40544200-40545400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
38	chr15:40544200-40545400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:40544200-40545400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:40544200-40545600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
41	chr15:40544200-40545600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:40544200-40545800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
43	chr15:40544200-40545800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
44	chr15:40544400-40544600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
45	chr15:40544400-40544600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
46	chr15:40544400-40544600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:40544400-40544600	Enhancers	Ovary	ovary
48	chr15:40544400-40544600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
49	chr15:40544400-40544600	Enhancers	NHEK	skin
50	chr15:40544400-40544800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin

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