Variant report

Variant	rs57064725
Chromosome Location	chr15:78833036-78833037
allele	A/C
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	TAF1	chr15:78832415-78833182	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:78832482-78833258	A549	lung:	n/a	n/a
3	YY1	chr15:78832583-78833218	NT2-D1	testis:	n/a	chr15:78833047-78833061 chr15:78832779-78832791 chr15:78833050-78833061
4	JUND	chr15:78832441-78833558	K562	blood:	n/a	chr15:78832738-78832747
5	SIN3AK20	chr15:78832466-78833259	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr15:78832980-78833130	GM12865	blood:	n/a	chr15:78833101-78833114
7	POLR2A	chr15:78832389-78833221	U87	brain:	n/a	n/a
8	ZBTB7A	chr15:78832887-78833242	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:78832434-78833075	HepG2	liver:	n/a	n/a
10	TAF1	chr15:78832373-78833230	ECC-1	luminal epithelium:	n/a	n/a
11	E2F4	chr15:78832329-78833108	MCF10A-Er-Src	breast:	n/a	chr15:78832739-78832748 chr15:78832769-78832778 chr15:78833049-78833058
12	FOXP2	chr15:78832500-78833160	PFSK-1	brain:	n/a	n/a
13	CTCF	chr15:78832940-78833090	GM12865	blood:	n/a	n/a
14	TAF1	chr15:78832430-78833334	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:78832370-78833100	K562	blood:	n/a	n/a
16	POLR2A	chr15:78832300-78833450	HUVEC	blood vessel:	n/a	n/a
17	CTCF	chr15:78832980-78833130	HRPEpiC	eye:	n/a	chr15:78833101-78833114
18	POLR2A	chr15:78832388-78833212	HCT-116	colon:	n/a	n/a
19	REST	chr15:78832450-78833098	A549	lung:	n/a	chr15:78832656-78832666
20	GATA2	chr15:78832738-78833831	SH-SY5Y	brain:	n/a	n/a
21	POLR2A	chr15:78832021-78833457	PFSK-1	brain:	n/a	n/a
22	MAX	chr15:78832479-78833520	SK-N-SH	brain:	n/a	chr15:78833105-78833115 chr15:78833118-78833128
23	MXI1	chr15:78832315-78833620	GM12878	blood:	n/a	n/a
24	SIN3AK20	chr15:78832516-78833342	K562	blood:	n/a	n/a
25	CTCF	chr15:78832980-78833130	HepG2	liver:	n/a	chr15:78833101-78833114
26	POLR2A	chr15:78832284-78834051	K562	blood:	n/a	n/a
27	ELF1	chr15:78832134-78833114	MCF-7	breast:	n/a	chr15:78832717-78832728 chr15:78832718-78832727
28	MAX	chr15:78832267-78833432	NB4	blood:	n/a	chr15:78833105-78833115 chr15:78833118-78833128
29	ZNF263	chr15:78832328-78833042	HEK293-T-REx	kidney:	n/a	n/a
30	EP300	chr15:78832446-78833128	GM12878	blood:	n/a	chr15:78833095-78833104 chr15:78833047-78833063 chr15:78833052-78833061 chr15:78832502-78832516 chr15:78832672-78832688 chr15:78833054-78833070
31	ZBTB7A	chr15:78832504-78833249	K562	blood:	n/a	n/a
32	POLR2A	chr15:78830840-78834174	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:78832400-78833576	NB4	blood:	n/a	n/a
34	TAF1	chr15:78832537-78833371	H1-hESC	embryonic stem cell:	n/a	n/a
35	MYC	chr15:78832270-78833718	K562	blood:	n/a	chr15:78833105-78833115 chr15:78833118-78833128
36	TAF1	chr15:78832251-78833566	A549	lung:	n/a	n/a
37	TAF1	chr15:78832500-78833100	Hela-S3	cervix:	n/a	n/a
38	CTCFL	chr15:78832961-78833173	K562	blood:	n/a	n/a
39	POLR2A	chr15:78832511-78833456	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr15:78832174-78833462	GM12892	blood:	n/a	n/a
41	YY1	chr15:78832531-78833316	K562	blood:	n/a	chr15:78833047-78833061 chr15:78832779-78832791 chr15:78833050-78833061
42	POLR2A	chr15:78832398-78833473	H1-hESC	embryonic stem cell:	n/a	n/a
43	YY1	chr15:78832426-78833303	H1-hESC	embryonic stem cell:	n/a	chr15:78833047-78833061 chr15:78832779-78832791 chr15:78833050-78833061
44	THAP1	chr15:78832657-78833109	K562	blood:	n/a	n/a
45	TBP	chr15:78832282-78833336	K562	blood:	n/a	n/a
46	CTCF	chr15:78832911-78833240	IMR90	lung:	n/a	chr15:78833101-78833114
47	CTCF	chr15:78833020-78833170	GM06990	blood:	n/a	chr15:78833101-78833114
48	RELA	chr15:78832407-78833377	GM19099	blood:	n/a	n/a
49	RELA	chr15:78832408-78833971	GM18951	blood:	n/a	n/a
50	PML	chr15:78832394-78833226	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78831297..78836398-chr15:78856605..78860226,12	MCF-7	breast:
2	chr15:78832604..78836535-chr15:78856473..78859290,6	MCF-7	breast:
3	chr10:113943131..113944016-chr15:78832161..78833133,2	NB4	blood:
4	chr15:78797464..78804546-chr15:78829529..78835433,12	MCF-7	breast:
5	chr15:78832891..78834488-chr15:78856612..78858995,2	K562	blood:
6	chr15:78832192..78833048-chr7:66205633..66206174,2	Hela-S3	cervix:
7	chr15:78832765..78833367-chr2:88315347..88316114,2	Hela-S3	cervix:
8	chr15:78798809..78800718-chr15:78830322..78833228,2	K562	blood:
9	chr15:78576883..78578539-chr15:78832474..78833981,2	MCF-7	breast:
10	chr15:78831312..78834277-chr15:78872379..78875019,2	MCF-7	breast:
11	chr15:78798844..78801827-chr15:78830907..78834394,5	MCF-7	breast:
12	chr15:78803621..78806940-chr15:78831151..78833237,3	K562	blood:
13	chr1:149858565..149859460-chr15:78832474..78833190,2	NB4	blood:
14	chr15:78832497..78833440-chr22:19419378..19420060,2	NB4	blood:
15	chr15:78832710..78833320-chr6:28303407..28304006,2	NB4	blood:
16	chr15:78831864..78834406-chr17:59476584..59478636,2	MCF-7	breast:
17	chr15:78832641..78833321-chr9:127631045..127631894,2	Hela-S3	cervix:
18	chr15:78798048..78801609-chr15:78828919..78833228,5	K562	blood:
19	chr15:78556899..78558870-chr15:78832501..78834304,2	MCF-7	breast:
20	chr15:78829726..78834442-chr15:78855710..78860360,8	K562	blood:
21	chr15:78729933..78731610-chr15:78832734..78835693,2	MCF-7	breast:
22	chr15:78832455..78833289-chr2:42275028..42275703,2	Hela-S3	cervix:
23	chr15:78832482..78833234-chr17:8113195..8113966,2	Hela-S3	cervix:

Variant related genes	Relation type
PSMA4	TF binding region
ENSG00000222724	Chromatin interaction
ENSG00000169684	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000188266	Chromatin interaction
ENSG00000136950	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000136381	Chromatin interaction
ENSG00000154710	Chromatin interaction
ENSG00000185608	Chromatin interaction
ENSG00000178999	Chromatin interaction
ENSG00000162878	Chromatin interaction
ENSG00000243335	Chromatin interaction
ENSG00000140395	Chromatin interaction
ENSG00000119927	Chromatin interaction
ENSG00000140403	Chromatin interaction
ENSG00000267280	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12438181	0.84[EUR][1000 genomes]
rs12438659	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12439240	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12441354	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12441426	0.85[EUR][1000 genomes]
rs2036534	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28437878	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28498264	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34138960	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34664138	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35212593	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3813570	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4461039	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs503464	0.81[EUR][1000 genomes]
rs59133824	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59683676	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61204066	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7163730	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7169584	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7181245	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7181447	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs905739	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1038816	chr15:78796434-78881087	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs57064725	IREB2	Cis_1M	lymphoblastoid	RTeQTL
rs57064725	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs57064725	PSMA4	cis	cerebellar cortex	BrainEAC
rs57064725	PSMA4	cis	intralobular white matter	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78832000-78833400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:78832000-78833800	Active TSS	Colon Smooth Muscle	Colon
3	chr15:78832000-78834200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:78832000-78834200	Active TSS	Duodenum Mucosa	Duodenum
5	chr15:78832000-78834600	Active TSS	Colonic Mucosa	Colon
6	chr15:78832200-78833200	Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr15:78832200-78833400	Active TSS	Primary T cells from cord blood	blood
8	chr15:78832200-78833400	Active TSS	Primary hematopoietic stem cells	blood
9	chr15:78832200-78833400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr15:78832200-78833400	Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr15:78832200-78833400	Active TSS	Brain Cingulate Gyrus	brain
12	chr15:78832200-78833400	Active TSS	Brain Germinal Matrix	brain
13	chr15:78832200-78833400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:78832200-78833400	Active TSS	Fetal Lung	lung
15	chr15:78832200-78833400	Active TSS	Stomach Smooth Muscle	stomach
16	chr15:78832200-78833400	Active TSS	Monocytes-CD14+_RO01746	blood
17	chr15:78832200-78833600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:78832200-78833600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:78832200-78833600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:78832200-78833600	Active TSS	Brain Angular Gyrus	brain
21	chr15:78832200-78833600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr15:78832200-78833600	Active TSS	Brain Substantia Nigra	brain
23	chr15:78832200-78833600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr15:78832200-78833600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr15:78832200-78833600	Active TSS	Fetal Brain Female	brain
26	chr15:78832200-78833600	Active TSS	Fetal Stomach	stomach
27	chr15:78832200-78833600	Active TSS	Spleen	Spleen
28	chr15:78832200-78833600	Active TSS	HUVEC	blood vessel
29	chr15:78832200-78833800	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr15:78832200-78833800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr15:78832200-78833800	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr15:78832200-78833800	Active TSS	Muscle Satellite Cultured Cells	--
33	chr15:78832200-78833800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:78832200-78833800	Active TSS	Fetal Intestine Small	intestine
35	chr15:78832200-78833800	Active TSS	Gastric	stomach
36	chr15:78832200-78833800	Active TSS	Rectal Smooth Muscle	rectum
37	chr15:78832200-78833800	Active TSS	Hela-S3	cervix
38	chr15:78832200-78834000	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr15:78832200-78834000	Active TSS	H1 Cell Line	embryonic stem cell
40	chr15:78832200-78834000	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr15:78832200-78834000	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr15:78832200-78834000	Active TSS	Fetal Intestine Large	intestine
43	chr15:78832200-78834000	Active TSS	Fetal Kidney	kidney
44	chr15:78832200-78834000	Active TSS	Placenta	Placenta
45	chr15:78832200-78834000	Active TSS	Left Ventricle	heart
46	chr15:78832200-78834000	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr15:78832200-78834000	Active TSS	Right Ventricle	heart
48	chr15:78832200-78834000	Active TSS	Stomach Mucosa	stomach
49	chr15:78832200-78834000	Active TSS	A549	lung
50	chr15:78832200-78834000	Active TSS	HMEC	breast

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