Variant report

Variant	rs12594158
Chromosome Location	chr15:75109953-75109954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr15:75109904-75109985	MCF-7	breast:	n/a	n/a
2	TEAD4	chr15:75109474-75110158	MCF-7	breast:	n/a	n/a
3	ESR1	chr15:75109031-75110123	T-47D	breast:	n/a	chr15:75109930-75109945 chr15:75109930-75109947
4	ELF1	chr15:75109268-75110145	MCF-7	breast:	n/a	n/a
5	SIN3AK20	chr15:75109006-75110213	MCF-7	breast:	n/a	n/a
6	SIN3AK20	chr15:75109331-75110162	MCF-7	breast:	n/a	n/a
7	RAD21	chr15:75109528-75110008	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAFK	chr15:75109810-75110085	HepG2	liver:	n/a	chr15:75109976-75109991 chr15:75109975-75109985
9	RAD21	chr15:75109634-75110006	HepG2	liver:	n/a	n/a
10	ESR1	chr15:75109107-75110177	T-47D	breast:	n/a	chr15:75109930-75109945 chr15:75109930-75109947
11	FOXA1	chr15:75109582-75109974	T-47D	breast:	n/a	n/a
12	EP300	chr15:75109377-75110162	MCF-7	breast:	n/a	n/a
13	CTCF	chr15:75109860-75110010	HFF-Myc	foreskin:	n/a	n/a
14	CTCF	chr15:75109435-75110148	MCF-7	breast:	n/a	n/a
15	HDAC2	chr15:75109520-75110138	MCF-7	breast:	n/a	n/a
16	MYC	chr15:75109854-75109973	MCF-7	breast:	n/a	n/a
17	ZNF263	chr15:75109364-75110110	HEK293-T-REx	kidney:	n/a	chr15:75110057-75110066
18	ESR1	chr15:75109301-75110059	T-47D	breast:	n/a	chr15:75109930-75109945 chr15:75109930-75109947
19	TCF12	chr15:75109105-75110205	MCF-7	breast:	n/a	chr15:75109212-75109222
20	MXI1	chr15:75109005-75110148	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr15:75109644-75109969	T-47D	breast:	n/a	n/a
22	GATA3	chr15:75108978-75110143	MCF-7	breast:	n/a	chr15:75109980-75109987
23	CTCF	chr15:75109655-75109967	NHEK	skin:	n/a	n/a
24	ESR1	chr15:75109546-75110083	T-47D	breast:	n/a	chr15:75109930-75109945 chr15:75109930-75109947
25	RAD21	chr15:75109665-75109956	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr15:75109434-75110180	MCF-7	breast:	n/a	n/a
27	ESR1	chr15:75109359-75110144	T-47D	breast:	n/a	chr15:75109930-75109945 chr15:75109930-75109947
28	HA-E2F1	chr15:75109368-75110048	MCF-7	breast:	n/a	n/a
29	ESR1	chr15:75109084-75110146	T-47D	breast:	n/a	chr15:75109930-75109945 chr15:75109930-75109947
30	TCF7L2	chr15:75109556-75109995	MCF-7	breast:	n/a	n/a
31	GATA3	chr15:75109191-75110084	MCF-7	breast:	n/a	chr15:75109980-75109987
32	MAFK	chr15:75109836-75110074	HepG2	liver:	n/a	chr15:75109976-75109991 chr15:75109975-75109985
33	RAD21	chr15:75109462-75110164	MCF-7	breast:	n/a	n/a
34	ZNF217	chr15:75109264-75110083	MCF-7	breast:	n/a	n/a
35	CTCF	chr15:75109507-75110107	MCF-7	breast:	n/a	n/a
36	NR2F2	chr15:75109054-75110170	MCF-7	breast:	n/a	n/a
37	EP300	chr15:75109524-75110022	T-47D	breast:	n/a	n/a
38	HDAC2	chr15:75109315-75110165	MCF-7	breast:	n/a	n/a
39	EP300	chr15:75109103-75110147	MCF-7	breast:	n/a	chr15:75109230-75109237
40	MXI1	chr15:75109723-75110047	HepG2	liver:	n/a	n/a
41	MAFF	chr15:75109758-75110065	HepG2	liver:	n/a	chr15:75109975-75109993
42	STAT3	chr15:75109939-75109998	MCF10A-Er-Src	breast:	n/a	n/a
43	CTCF	chr15:75109642-75110000	HepG2	liver:	n/a	n/a
44	FOS	chr15:75109849-75110045	MCF10A-Er-Src	breast:	n/a	chr15:75109976-75109986
45	GATA3	chr15:75109258-75110185	MCF-7	breast:	n/a	chr15:75109980-75109987
46	RAD21	chr15:75109551-75110048	HepG2	liver:	n/a	n/a
47	MAX	chr15:75109162-75110109	MCF-7	breast:	n/a	n/a
48	MYC	chr15:75109710-75110012	MCF-7	breast:	n/a	n/a
49	FOXM1	chr15:75109232-75110140	MCF-7	breast:	n/a	n/a
50	MYC	chr15:75109851-75110036	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75109328..75110019-chr15:75193813..75194663,2	MCF-7	breast:
2	chr15:75109529..75110053-chr15:75194068..75194696,2	MCF-7	breast:
3	chr15:75109649..75110485-chr15:75229607..75230565,3	MCF-7	breast:
4	chr15:75074156..75079604-chr15:75107384..75112501,9	MCF-7	breast:
5	chr1:150951967..150952513-chr15:75109160..75110043,2	MCF-7	breast:
6	chr15:75109403..75110158-chr15:75139541..75140351,8	MCF-7	breast:
7	chr15:75063364..75063990-chr15:75109881..75110560,2	MCF-7	breast:
8	chr15:75092200..75093072-chr15:75108800..75110484,5	MCF-7	breast:
9	chr15:75063049..75063972-chr15:75109525..75110306,2	MCF-7	breast:
10	chr15:75109533..75111240-chr15:75228886..75230754,2	MCF-7	breast:
11	chr15:75109449..75112132-chr15:75112266..75114045,2	MCF-7	breast:
12	chr15:75062932..75063974-chr15:75109427..75110288,5	MCF-7	breast:
13	chr15:74002241..74003107-chr15:75109478..75110334,3	MCF-7	breast:
14	chr15:75081065..75082080-chr15:75109443..75110385,9	MCF-7	breast:
15	chr15:75081235..75085402-chr15:75108223..75111318,4	MCF-7	breast:
16	chr15:75081323..75082242-chr15:75109443..75110385,9	MCF-7	breast:
17	chr15:75072350..75078841-chr15:75107920..75114107,12	MCF-7	breast:
18	chr15:75109188..75110335-chr15:75127274..75128567,6	MCF-7	breast:
19	chr15:75109649..75110485-chr15:75229607..75230565,5	MCF-7	breast:
20	chr15:75062932..75063974-chr15:75109427..75110335,6	MCF-7	breast:
21	chr15:75109469..75110121-chr15:75139541..75140329,6	MCF-7	breast:
22	chr15:75109719..75111456-chr15:75185022..75186522,2	MCF-7	breast:
23	chr15:74907471..74909461-chr15:75108949..75111187,2	MCF-7	breast:
24	chr15:75108356..75114001-chr15:75126388..75130558,9	MCF-7	breast:
25	chr15:75109652..75112640-chr15:76193633..76196409,2	K562	blood:
26	chr15:75106165..75113668-chr15:75132311..75136608,10	MCF-7	breast:
27	chr15:75109533..75110332-chr15:75134854..75135663,2	MCF-7	breast:
28	chr15:75109829..75110505-chr15:75121077..75121887,4	MCF-7	breast:
29	chr15:75080218..75087203-chr15:75106250..75113071,13	MCF-7	breast:
30	chr15:75107985..75111072-chr15:75197111..75200997,5	MCF-7	breast:

No data

Variant related genes	Relation type
LMAN1L	TF binding region
ENSG00000261606	TF binding region
ENSG00000103653	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000167196	Chromatin interaction
ENSG00000264386	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000179335	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12439525	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12439944	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12441444	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12443172	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593251	0.89[ASN][1000 genomes]
rs1531162	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1531163	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16972714	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2229730	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28397782	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28431073	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28577988	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28583379	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2899827	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3743486	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743487	0.84[EUR][1000 genomes]
rs3803568	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886409	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4886620	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8039046	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9796628	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv520527	chr15:75108636-75122856	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75097600-75111000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr15:75101800-75113200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:75107000-75112200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr15:75107200-75110000	Enhancers	Colon Smooth Muscle	Colon
5	chr15:75107200-75111200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr15:75107200-75111400	Enhancers	Esophagus	oesophagus
7	chr15:75107200-75111800	Enhancers	Colonic Mucosa	Colon
8	chr15:75107200-75112400	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr15:75107200-75114400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:75108000-75113000	Weak transcription	Right Atrium	heart
11	chr15:75108200-75111000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:75108200-75111000	Weak transcription	GM12878-XiMat	blood
13	chr15:75108200-75111400	Weak transcription	HSMMtube	muscle
14	chr15:75108400-75110400	Weak transcription	Gastric	stomach
15	chr15:75108400-75110600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr15:75108600-75110000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr15:75108600-75110600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr15:75108600-75111400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:75108600-75111600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:75108800-75110000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr15:75108800-75110000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr15:75108800-75110600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:75108800-75111400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:75108800-75112600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:75109000-75110000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr15:75109000-75110000	Enhancers	Fetal Brain Male	brain
27	chr15:75109000-75110000	Enhancers	Fetal Intestine Large	intestine
28	chr15:75109000-75110000	Flanking Active TSS	HepG2	liver
29	chr15:75109000-75110800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr15:75109000-75111400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr15:75109000-75111600	Enhancers	Placenta	Placenta
32	chr15:75109000-75111600	Enhancers	HMEC	breast
33	chr15:75109000-75111800	Enhancers	Spleen	Spleen
34	chr15:75109200-75110000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr15:75109200-75110000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:75109200-75110000	Enhancers	Brain Germinal Matrix	brain
37	chr15:75109200-75110000	Enhancers	Fetal Heart	heart
38	chr15:75109200-75110000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr15:75109200-75110000	Flanking Active TSS	Hela-S3	cervix
40	chr15:75109200-75111600	Enhancers	NHEK	skin
41	chr15:75109200-75112000	Enhancers	Duodenum Mucosa	Duodenum
42	chr15:75109400-75110000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr15:75109400-75110000	Bivalent Enhancer	Fetal Stomach	stomach
44	chr15:75109400-75110000	Enhancers	Stomach Smooth Muscle	stomach
45	chr15:75109400-75110200	Enhancers	Fetal Intestine Small	intestine
46	chr15:75109400-75111200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:75109400-75111600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:75109400-75111600	Enhancers	Lung	lung
49	chr15:75109400-75111600	Enhancers	Right Ventricle	heart
50	chr15:75109400-75111600	Enhancers	Stomach Mucosa	stomach

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