Variant report

Variant	rs12915092
Chromosome Location	chr15:56035767-56035768
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	ZBTB7A	chr15:56035235-56035782	HepG2	liver:	n/a	chr15:56035663-56035671
2	PBX3	chr15:56035051-56035826	A549	lung:	n/a	n/a
3	GATA2	chr15:56035216-56036671	SH-SY5Y	brain:	n/a	n/a
4	SMARCB1	chr15:56033753-56036042	Hela-S3	cervix:	n/a	n/a
5	CHD2	chr15:56035023-56035769	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:56033776-56035901	HepG2	liver:	n/a	n/a
7	RAD21	chr15:56034820-56035979	SK-N-SH_RA	brain:	n/a	chr15:56035363-56035375 chr15:56035488-56035502 chr15:56035337-56035347 chr15:56035361-56035374
8	TEAD4	chr15:56035104-56035871	SK-N-SH	brain:	n/a	n/a
9	EP300	chr15:56034966-56035910	SK-N-SH	brain:	n/a	chr15:56035184-56035193 chr15:56035357-56035373 chr15:56035372-56035381 chr15:56035458-56035467
10	TCF12	chr15:56034098-56036186	A549	lung:	n/a	chr15:56034864-56034871 chr15:56036136-56036146
11	POLR2A	chr15:56034590-56035781	A549	lung:	n/a	n/a
12	MAX	chr15:56034182-56035795	HepG2	liver:	n/a	chr15:56034634-56034641 chr15:56035766-56035776 chr15:56035588-56035598 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
13	MXI1	chr15:56032346-56036713	SK-N-SH	brain:	n/a	chr15:56034632-56034641
14	POLR2A	chr15:56034978-56035806	PANC-1	pancreas:	n/a	n/a
15	MAX	chr15:56034264-56035835	HepG2	liver:	n/a	chr15:56034634-56034641 chr15:56035766-56035776 chr15:56035588-56035598 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
16	ZBTB7A	chr15:56034630-56036028	ECC-1	luminal epithelium:	n/a	chr15:56035663-56035671
17	POLR2A	chr15:56034869-56035902	HepG2	liver:	n/a	n/a
18	TAF1	chr15:56034606-56035776	ECC-1	luminal epithelium:	n/a	n/a
19	PBX3	chr15:56034881-56035771	A549	lung:	n/a	n/a
20	SIN3AK20	chr15:56035042-56035807	MCF-7	breast:	n/a	n/a
21	CREB1	chr15:56034671-56035908	HepG2	liver:	n/a	n/a
22	MAZ	chr15:56034404-56035856	IMR90	lung:	n/a	chr15:56034634-56034641 chr15:56035766-56035776 chr15:56035588-56035598 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
23	PBX3	chr15:56035078-56035834	SK-N-SH	brain:	n/a	n/a
24	MAX	chr15:56034188-56035828	A549	lung:	n/a	chr15:56034634-56034641 chr15:56035766-56035776 chr15:56035588-56035598 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
25	GATA3	chr15:56034863-56035790	A549	lung:	n/a	n/a
26	SIN3AK20	chr15:56034267-56035773	PANC-1	pancreas:	n/a	n/a
27	MAX	chr15:56034103-56035956	A549	lung:	n/a	chr15:56034634-56034641 chr15:56035766-56035776 chr15:56035588-56035598 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
28	POLR2A	chr15:56034913-56035895	SK-N-SH	brain:	n/a	n/a
29	CREB1	chr15:56034531-56035816	A549	lung:	n/a	n/a
30	YY1	chr15:56034407-56035829	HepG2	liver:	n/a	chr15:56035667-56035678 chr15:56035587-56035596 chr15:56035392-56035401 chr15:56035152-56035163 chr15:56035372-56035381 chr15:56035393-56035407 chr15:56035369-56035378 chr15:56035706-56035717 chr15:56035373-56035384 chr15:56034581-56034595 chr15:56035392-56035403 chr15:56035363-56035377 chr15:56035186-56035200
31	TAF1	chr15:56035055-56035772	A549	lung:	n/a	n/a
32	POLR2A	chr15:56034829-56035982	PFSK-1	brain:	n/a	n/a
33	POLR2A	chr15:56035102-56035780	HepG2	liver:	n/a	n/a
34	POLR2A	chr15:56034972-56035804	PFSK-1	brain:	n/a	n/a
35	MAZ	chr15:56034711-56035888	HepG2	liver:	n/a	chr15:56035766-56035776 chr15:56035588-56035598 chr15:56035366-56035376
36	POLR2A	chr15:56034966-56035781	ECC-1	luminal epithelium:	n/a	n/a
37	TAF1	chr15:56035093-56035851	ECC-1	luminal epithelium:	n/a	n/a
38	PBX3	chr15:56035117-56035774	SK-N-SH	brain:	n/a	n/a
39	ZBTB7A	chr15:56034418-56036029	ECC-1	luminal epithelium:	n/a	chr15:56034584-56034593 chr15:56035663-56035671
40	POLR2A	chr15:56034423-56035801	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:56033858..56036761-chr15:56051440..56053715,2	MCF-7	breast:
2	chr1:109645681..109648514-chr15:56034152..56035869,2	MCF-7	breast:
3	chr15:56034248..56036795-chr15:56038057..56039658,2	MCF-7	breast:

Variant related genes	Relation type
PRTG	TF binding region
ENSG00000259369	TF binding region
ENSG00000251484	Chromatin interaction
ENSG00000221218	Chromatin interaction
ENSG00000259369	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1011061	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10152116	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10152830	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10851590	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11071203	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11071204	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11632579	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11632762	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11639086	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11852746	0.90[ASN][1000 genomes]
rs11853533	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11857254	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11857271	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12438264	0.83[AFR][1000 genomes]
rs12438394	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12439011	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12440103	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12442165	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12899647	0.90[ASN][1000 genomes]
rs12899976	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12901963	0.90[ASN][1000 genomes]
rs12903239	0.90[ASN][1000 genomes]
rs12905693	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12906885	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12907557	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12907772	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12907892	0.90[ASN][1000 genomes]
rs12908232	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12908813	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12910180	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12911682	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12912118	0.81[ASN][1000 genomes]
rs12914863	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915423	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34303822	0.90[ASN][1000 genomes]
rs3985768	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4412917	0.90[ASN][1000 genomes]
rs4774222	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55874929	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66519039	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8028880	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv1052495	chr15:56013617-56102164	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3390617	chr15:56034285-56036833	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56031400-56036600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:56032600-56036200	Active TSS	Fetal Kidney	kidney
3	chr15:56033200-56036000	Active TSS	Placenta Amnion	Placenta Amnion
4	chr15:56033400-56036200	Active TSS	Ovary	ovary
5	chr15:56033600-56035800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:56033600-56035800	Active TSS	Fetal Intestine Large	intestine
7	chr15:56033600-56035800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
8	chr15:56033600-56035800	Active TSS	Lung	lung
9	chr15:56033600-56036000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:56033600-56036000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr15:56033600-56036000	Active TSS	Aorta	Aorta
12	chr15:56033600-56036000	Active TSS	Right Ventricle	heart
13	chr15:56033600-56036200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
14	chr15:56033800-56035800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:56033800-56035800	Active TSS	Gastric	stomach
16	chr15:56034000-56035800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:56034000-56035800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:56034000-56035800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:56034000-56036000	Active TSS	A549	lung
20	chr15:56034000-56036200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr15:56034200-56036000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:56034200-56036000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:56034200-56036000	Active TSS	Left Ventricle	heart
24	chr15:56034200-56036200	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr15:56034200-56036200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
26	chr15:56034200-56036200	Active TSS	Fetal Lung	lung
27	chr15:56034400-56035800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:56034400-56035800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:56034400-56035800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
30	chr15:56034400-56035800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr15:56034400-56035800	Active TSS	NHLF	lung
32	chr15:56034400-56036000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr15:56034400-56036000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:56034400-56036000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:56034400-56036000	Active TSS	Hela-S3	cervix
36	chr15:56034400-56036000	Active TSS	HSMM	muscle
37	chr15:56034400-56036000	Active TSS	HSMMtube	muscle
38	chr15:56034400-56036200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
39	chr15:56034400-56036200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:56034400-56036200	Active TSS	Brain Substantia Nigra	brain
41	chr15:56034400-56036400	Active TSS	Stomach Smooth Muscle	stomach
42	chr15:56034400-56036600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
43	chr15:56034600-56035800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
44	chr15:56034600-56035800	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr15:56034600-56035800	Flanking Active TSS	Liver	Liver
46	chr15:56034600-56035800	Bivalent/Poised TSS	Esophagus	oesophagus
47	chr15:56034600-56035800	Bivalent/Poised TSS	Fetal Stomach	stomach
48	chr15:56034600-56035800	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr15:56034600-56035800	Active TSS	HUVEC	blood vessel
50	chr15:56034600-56036000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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