Variant report

Variant	rs55931072
Chromosome Location	chr15:52385827-52385828
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	JUND	chr15:52385500-52386690	Hela-S3	cervix:	n/a	chr15:52386528-52386539
2	MEF2A	chr15:52385595-52386612	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr15:52385520-52386381	HUVEC	blood vessel:	n/a	n/a
4	CHD2	chr15:52385372-52386795	Hela-S3	cervix:	n/a	n/a
5	GATA3	chr15:52385378-52386862	A549	lung:	n/a	chr15:52385912-52385920
6	GATA2	chr15:52385126-52386736	HUVEC	blood vessel:	n/a	chr15:52385912-52385920
7	TEAD4	chr15:52385727-52386365	ECC-1	luminal epithelium:	n/a	n/a
8	NR3C1	chr15:52385652-52386404	A549	lung:	n/a	n/a
9	EP300	chr15:52385530-52386631	A549	lung:	n/a	chr15:52385603-52385612
10	TEAD4	chr15:52385465-52386503	A549	lung:	n/a	n/a
11	STAT3	chr15:52385644-52386308	MCF10A-Er-Src	breast:	n/a	chr15:52385946-52385953 chr15:52385794-52385803
12	MYC	chr15:52385822-52385925	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr15:52385565-52386444	SK-N-SH	brain:	n/a	n/a
14	STAT3	chr15:52385690-52386313	MCF10A-Er-Src	breast:	n/a	chr15:52385946-52385953 chr15:52385794-52385803
15	FOSL2	chr15:52385433-52386696	SK-N-SH	brain:	n/a	chr15:52386528-52386539
16	EP300	chr15:52385640-52386455	SK-N-SH_RA	brain:	n/a	n/a
17	MAX	chr15:52385376-52386765	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr15:52385488-52386833	Hela-S3	cervix:	n/a	n/a
19	TAF1	chr15:52385615-52386406	SK-N-SH	brain:	n/a	n/a
20	FOS	chr15:52385614-52386399	MCF10A-Er-Src	breast:	n/a	chr15:52385792-52385803
21	ATF3	chr15:52385569-52386433	A549	lung:	n/a	n/a
22	EP300	chr15:52385393-52386652	Hela-S3	cervix:	n/a	chr15:52385603-52385612
23	NFIC	chr15:52385415-52386765	SK-N-SH	brain:	n/a	n/a
24	PBX3	chr15:52385478-52386768	SK-N-SH	brain:	n/a	n/a
25	FOS	chr15:52385636-52386393	MCF10A-Er-Src	breast:	n/a	chr15:52385792-52385803
26	JUND	chr15:52385583-52386620	SK-N-SH	brain:	n/a	chr15:52386528-52386539
27	TFAP2C	chr15:52385510-52386739	Hela-S3	cervix:	n/a	n/a
28	MAX	chr15:52385460-52386548	A549	lung:	n/a	n/a
29	SIN3AK20	chr15:52385558-52386530	SK-N-SH	brain:	n/a	n/a
30	JUND	chr15:52385472-52386603	SK-N-SH	brain:	n/a	chr15:52386528-52386539
31	GATA3	chr15:52385457-52386788	SK-N-SH	brain:	n/a	chr15:52385912-52385920
32	CEBPB	chr15:52385294-52386852	Hela-S3	cervix:	n/a	n/a
33	ELK4	chr15:52385558-52386196	Hela-S3	cervix:	n/a	n/a
34	FOS	chr15:52385627-52386386	Hela-S3	cervix:	n/a	chr15:52385792-52385803
35	STAT3	chr15:52385532-52386397	MCF10A-Er-Src	breast:	n/a	chr15:52386336-52386347 chr15:52385946-52385953 chr15:52385794-52385803
36	MAFK	chr15:52385650-52386361	IMR90	lung:	n/a	chr15:52385795-52385804
37	NR3C1	chr15:52385570-52386694	A549	lung:	n/a	chr15:52386632-52386641 chr15:52386632-52386645
38	TCF12	chr15:52385044-52387001	SK-N-SH	brain:	n/a	chr15:52386512-52386520
39	REST	chr15:52385636-52386356	SK-N-SH	brain:	n/a	n/a
40	TAF1	chr15:52385558-52386333	Hela-S3	cervix:	n/a	n/a
41	MAX	chr15:52385349-52386761	SK-N-SH	brain:	n/a	n/a
42	RAD21	chr15:52385657-52385993	SK-N-SH_RA	brain:	n/a	n/a
43	POLR2A	chr15:52385591-52386052	HUVEC	blood vessel:	n/a	n/a
44	TCF7L2	chr15:52385676-52386802	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr15:52385817-52386586	U87	brain:	n/a	n/a
46	POLR2A	chr15:52385645-52386298	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr15:52385699-52386048	HUVEC	blood vessel:	n/a	n/a
48	E2F6	chr15:52385379-52386536	A549	lung:	n/a	n/a
49	MAX	chr15:52385411-52386779	Hela-S3	cervix:	n/a	n/a
50	PRDM1	chr15:52385546-52386213	Hela-S3	cervix:	n/a	chr15:52385731-52385744

No.	Distal block	Cell Line	Cell type
1	chr15:52381490..52382992-chr15:52383645..52386424,2	K562	blood:
2	chr15:52309194..52314432-chr15:52385325..52393461,10	MCF-7	breast:
3	chr15:52369845..52371701-chr15:52385019..52386714,2	MCF-7	breast:
4	chr15:52385731..52388322-chr15:52391743..52394058,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242327	TF binding region
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000259712	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12050787	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12438375	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12439046	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17706513	0.94[ASN][1000 genomes]
rs58510474	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58555938	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7173725	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52384600-52387600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:52384800-52386000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:52384800-52386600	Enhancers	Primary hematopoietic stem cells	blood
4	chr15:52384800-52387600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr15:52384800-52388200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:52385000-52386600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr15:52385000-52386800	Enhancers	Placenta	Placenta
8	chr15:52385000-52387600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr15:52385000-52387800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:52385000-52387800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:52385000-52387800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:52385000-52387800	Enhancers	NHLF	lung
13	chr15:52385000-52388400	Enhancers	HMEC	breast
14	chr15:52385200-52386200	Enhancers	Rectal Smooth Muscle	rectum
15	chr15:52385200-52386400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr15:52385200-52386800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:52385200-52387600	Enhancers	Fetal Muscle Leg	muscle
18	chr15:52385200-52387600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr15:52385400-52386000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr15:52385400-52386200	Flanking Active TSS	NH-A	brain
21	chr15:52385400-52386400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:52385400-52386400	Enhancers	Stomach Smooth Muscle	stomach
23	chr15:52385400-52386600	Flanking Active TSS	A549	lung
24	chr15:52385400-52386800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:52385400-52386800	Flanking Active TSS	NHEK	skin
26	chr15:52385400-52386800	Flanking Active TSS	Osteobl	bone
27	chr15:52385400-52387000	Flanking Active TSS	HSMM	muscle
28	chr15:52385400-52387600	Enhancers	Colon Smooth Muscle	Colon
29	chr15:52385400-52387600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr15:52385400-52387600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr15:52385400-52387600	Flanking Active TSS	NHDF-Ad	bronchial
32	chr15:52385400-52387800	Enhancers	Ovary	ovary
33	chr15:52385400-52387800	Flanking Active TSS	Hela-S3	cervix
34	chr15:52385600-52386000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:52385600-52386000	Enhancers	HUVEC	blood vessel
36	chr15:52385600-52386000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr15:52385600-52386200	Enhancers	Fetal Lung	lung
38	chr15:52385600-52386200	Flanking Active TSS	HSMMtube	muscle
39	chr15:52385600-52386400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:52385600-52386600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:52385600-52386600	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr15:52385600-52387200	Enhancers	HepG2	liver
43	chr15:52385600-52387800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr15:52385600-52388000	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr15:52385800-52386000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr15:52385800-52386200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:52385800-52386400	Enhancers	Fetal Muscle Trunk	muscle
48	chr15:52385800-52386600	Enhancers	Right Ventricle	heart
49	chr15:52385800-52387200	Enhancers	Pancreas	Pancrea
50	chr15:52385800-52387200	Enhancers	Psoas Muscle	Psoas

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