Variant report

Variant	rs12905521
Chromosome Location	chr15:74492820-74492821
allele	A/T
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	TCF7L2	chr15:74492602-74493793	Hela-S3	cervix:	n/a	n/a
2	MAFK	chr15:74492742-74493714	Hela-S3	cervix:	n/a	n/a
3	BATF	chr15:74492765-74493061	GM12878	blood:	n/a	chr15:74492924-74492935
4	MAX	chr15:74492613-74493813	Hela-S3	cervix:	n/a	chr15:74492902-74492911 chr15:74493646-74493656
5	TCF7L2	chr15:74492710-74493111	MCF-7	breast:	n/a	n/a
6	FOS	chr15:74492720-74493799	Hela-S3	cervix:	n/a	chr15:74492959-74492968 chr15:74492926-74492938 chr15:74492928-74492936
7	FOSL2	chr15:74492658-74493233	MCF-7	breast:	n/a	chr15:74492959-74492968 chr15:74492926-74492938 chr15:74492928-74492936
8	BCL3	chr15:74492637-74493293	A549	lung:	n/a	chr15:74492969-74492978
9	EBF1	chr15:74492707-74493078	GM12878	blood:	n/a	chr15:74492972-74492983 chr15:74492914-74492925 chr15:74492915-74492925
10	HDAC2	chr15:74492670-74493852	MCF-7	breast:	n/a	n/a
11	CHD2	chr15:74492673-74494429	Hela-S3	cervix:	n/a	n/a
12	NR3C1	chr15:74492594-74493219	A549	lung:	n/a	chr15:74492928-74492937 chr15:74492927-74492936
13	FOXM1	chr15:74492692-74493169	GM12878	blood:	n/a	n/a
14	TCF7L2	chr15:74492646-74493327	PANC-1	pancreas:	n/a	n/a
15	SMARCB1	chr15:74492604-74494571	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr15:74492570-74493235	MCF-7	breast:	n/a	n/a
17	JUND	chr15:74492682-74493697	Hela-S3	cervix:	n/a	chr15:74492959-74492968 chr15:74492926-74492938 chr15:74492926-74492937 chr15:74492928-74492936
18	MYC	chr15:74492742-74492940	NB4	blood:	n/a	chr15:74492902-74492911
19	CEBPB	chr15:74492740-74493117	A549	lung:	n/a	n/a
20	FOSL2	chr15:74492752-74493101	A549	lung:	n/a	chr15:74492959-74492968 chr15:74492926-74492938 chr15:74492928-74492936
21	EP300	chr15:74492620-74493076	MCF-7	breast:	n/a	n/a
22	POLR2A	chr15:74492754-74493077	U87	brain:	n/a	n/a
23	CEBPB	chr15:74492780-74493013	H1-hESC	embryonic stem cell:	n/a	n/a
24	TFAP2C	chr15:74492581-74495035	Hela-S3	cervix:	n/a	chr15:74493490-74493505 chr15:74492911-74492926
25	CEBPB	chr15:74492569-74494496	Hela-S3	cervix:	n/a	n/a
26	CEBPB	chr15:74492746-74493094	HepG2	liver:	n/a	n/a
27	RFX5	chr15:74492738-74493765	Hela-S3	cervix:	n/a	n/a
28	SMARCC1	chr15:74492611-74495990	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr15:74492662-74493110	GM12878	blood:	n/a	n/a
30	POLR2A	chr15:74492682-74493144	U87	brain:	n/a	n/a
31	POLR2A	chr15:74492708-74493091	HCT-116	colon:	n/a	n/a
32	NR3C1	chr15:74492649-74493060	A549	lung:	n/a	chr15:74492928-74492937 chr15:74492927-74492936
33	SP1	chr15:74492615-74493319	A549	lung:	n/a	n/a
34	YY1	chr15:74492758-74493005	HCT-116	colon:	n/a	n/a
35	JUND	chr15:74492571-74493267	HCT-116	colon:	n/a	chr15:74492959-74492968 chr15:74492926-74492938 chr15:74492926-74492937 chr15:74492928-74492936
36	PML	chr15:74492671-74493185	GM12878	blood:	n/a	n/a
37	EBF1	chr15:74492708-74493148	GM12878	blood:	n/a	chr15:74492972-74492983 chr15:74492914-74492925 chr15:74492915-74492925
38	NFIC	chr15:74492702-74493223	GM12878	blood:	n/a	n/a
39	RAD21	chr15:74492717-74493078	SK-N-SH_RA	brain:	n/a	n/a
40	STAT3	chr15:74492684-74493632	Hela-S3	cervix:	n/a	n/a
41	MXI1	chr15:74492650-74493809	Hela-S3	cervix:	n/a	n/a
42	ATF3	chr15:74492667-74493149	A549	lung:	n/a	n/a
43	IKZF1	chr15:74492771-74493094	GM12878	blood:	n/a	n/a
44	RCOR1	chr15:74492582-74494497	Hela-S3	cervix:	n/a	n/a
45	CEBPB	chr15:74492534-74493369	HCT-116	colon:	n/a	n/a
46	TCF7L2	chr15:74492694-74493073	HCT-116	colon:	n/a	n/a
47	FOS	chr15:74492705-74493327	MCF10A-Er-Src	breast:	n/a	chr15:74492959-74492968 chr15:74492926-74492938 chr15:74492928-74492936
48	NR3C1	chr15:74492725-74493120	A549	lung:	n/a	chr15:74492928-74492937 chr15:74492927-74492936
49	CREB1	chr15:74492781-74493018	A549	lung:	n/a	n/a
50	MYC	chr15:74492811-74493363	MCF10A-Er-Src	breast:	n/a	chr15:74492902-74492911

No.	Distal block	Cell Line	Cell type
1	chr15:74491398..74493100-chr15:74498606..74500534,2	MCF-7	breast:
2	chr15:74478980..74480513-chr15:74491993..74494403,2	MCF-7	breast:
3	chr15:74483852..74487473-chr15:74489633..74493518,4	K562	blood:
4	chr15:74481853..74488513-chr15:74489689..74497281,13	MCF-7	breast:
5	chr15:74209119..74211492-chr15:74491566..74493612,2	MCF-7	breast:
6	chr15:74421502..74423343-chr15:74491775..74494417,2	MCF-7	breast:

Variant related genes	Relation type
STRA6	TF binding region
ENSG00000259264	TF binding region
ENSG00000248540	Chromatin interaction
ENSG00000167178	Chromatin interaction
ENSG00000137868	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11630924	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11631509	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11633687	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639369	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11857410	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12911581	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12912258	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12915891	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34147822	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34234753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34573746	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34591452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35036456	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351242	0.86[EUR][1000 genomes]
rs35255788	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35917667	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62003660	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62003661	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72747610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733163	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs971755	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs971756	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs971757	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74469400-74493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:74485400-74493000	Weak transcription	Fetal Thymus	thymus
3	chr15:74489200-74509600	Weak transcription	Gastric	stomach
4	chr15:74489400-74499000	Weak transcription	Brain Anterior Caudate	brain
5	chr15:74490200-74493800	Weak transcription	Colonic Mucosa	Colon
6	chr15:74490600-74496200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:74490800-74493000	Enhancers	NH-A	brain
8	chr15:74491000-74503200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:74491400-74494800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:74491600-74494000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:74491600-74494000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:74491600-74494200	Enhancers	Fetal Intestine Large	intestine
13	chr15:74492000-74493400	Genic enhancers	Fetal Intestine Small	intestine
14	chr15:74492000-74496800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:74492400-74495000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr15:74492600-74493000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr15:74492600-74493000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr15:74492600-74493000	Enhancers	Osteobl	bone
19	chr15:74492600-74493200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:74492600-74493200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr15:74492600-74493200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr15:74492600-74493200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr15:74492600-74493400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr15:74492600-74493400	Enhancers	Stomach Smooth Muscle	stomach
25	chr15:74492600-74493800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:74492600-74493800	Enhancers	Fetal Stomach	stomach
27	chr15:74492600-74494000	Enhancers	Left Ventricle	heart
28	chr15:74492600-74494200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:74492600-74494200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr15:74492600-74494200	Enhancers	Adipose Nuclei	Adipose
31	chr15:74492600-74494200	Enhancers	HSMM	muscle
32	chr15:74492600-74494400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:74492600-74494600	Enhancers	Esophagus	oesophagus
34	chr15:74492600-74494600	Enhancers	Spleen	Spleen
35	chr15:74492600-74494800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:74492600-74494800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:74492600-74494800	Flanking Active TSS	A549	lung
38	chr15:74492600-74494800	Enhancers	NHEK	skin
39	chr15:74492600-74495000	Enhancers	Right Atrium	heart
40	chr15:74492600-74495000	Enhancers	NHDF-Ad	bronchial
41	chr15:74492600-74495400	Flanking Active TSS	Placenta	Placenta
42	chr15:74492600-74495400	Enhancers	Right Ventricle	heart
43	chr15:74492600-74495600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:74492600-74495800	Flanking Active TSS	Hela-S3	cervix
45	chr15:74492600-74496200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:74492600-74496400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:74492600-74496400	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr15:74492600-74496600	Enhancers	HMEC	breast
49	chr15:74492600-74496800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:74492600-74497000	Enhancers	Ovary	ovary

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