Variant report

Variant	rs73393497
Chromosome Location	chr15:39722325-39722326
allele	C/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	FOS	chr15:39722230-39722345	MCF10A-Er-Src	breast:	n/a	chr15:39722313-39722325 chr15:39722311-39722322 chr15:39722256-39722268
2	POLR2A	chr15:39722069-39722500	HUVEC	blood vessel:	n/a	n/a
3	NR2F2	chr15:39722081-39722580	MCF-7	breast:	n/a	n/a
4	POLR2A	chr15:39721938-39723507	HUVEC	blood vessel:	n/a	n/a
5	ATF2	chr15:39722020-39722552	GM12878	blood:	n/a	n/a
6	EP300	chr15:39722064-39722567	SK-N-SH_RA	brain:	n/a	chr15:39722128-39722142
7	RAD21	chr15:39722164-39722497	SK-N-SH_RA	brain:	n/a	n/a
8	CTCF	chr15:39722180-39722330	HCPEpiC	choroid plexus:	n/a	n/a
9	RAD21	chr15:39722142-39722666	IMR90	lung:	n/a	n/a
10	BHLHE40	chr15:39721937-39722434	GM12878	blood:	n/a	n/a
11	GATA3	chr15:39722018-39722648	MCF-7	breast:	n/a	chr15:39722476-39722486 chr15:39722130-39722140 chr15:39722316-39722325
12	PBX3	chr15:39722045-39722609	SK-N-SH	brain:	n/a	n/a
13	NR2F2	chr15:39722145-39722578	MCF-7	breast:	n/a	n/a
14	SPI1	chr15:39722021-39722616	GM12891	blood:	n/a	chr15:39722133-39722142 chr15:39722118-39722131
15	GATA3	chr15:39721977-39722657	SK-N-SH	brain:	n/a	chr15:39722476-39722486 chr15:39722130-39722140 chr15:39722316-39722325
16	PBX3	chr15:39722023-39722632	SK-N-SH	brain:	n/a	n/a
17	USF2	chr15:39722193-39722378	Hela-S3	cervix:	n/a	n/a
18	GATA3	chr15:39722017-39722695	MCF-7	breast:	n/a	chr15:39722476-39722486 chr15:39722130-39722140 chr15:39722316-39722325
19	MEF2C	chr15:39721908-39722375	GM12878	blood:	n/a	chr15:39722132-39722140 chr15:39722106-39722121 chr15:39722103-39722124
20	TCF12	chr15:39722003-39722666	SK-N-SH	brain:	n/a	n/a
21	GATA3	chr15:39722052-39722606	A549	lung:	n/a	chr15:39722476-39722486 chr15:39722130-39722140 chr15:39722316-39722325
22	EP300	chr15:39721985-39722514	GM12878	blood:	n/a	chr15:39722128-39722142
23	EP300	chr15:39721979-39722539	GM12878	blood:	n/a	chr15:39722128-39722142
24	BATF	chr15:39721949-39722530	GM12878	blood:	n/a	n/a
25	GATA3	chr15:39721830-39722716	SK-N-SH	brain:	n/a	chr15:39722476-39722486 chr15:39722130-39722140 chr15:39722316-39722325
26	FOXA2	chr15:39722220-39722571	A549	lung:	n/a	n/a
27	TCF7L2	chr15:39722116-39722458	MCF-7	breast:	n/a	n/a
28	BRCA1	chr15:39722260-39722519	Hela-S3	cervix:	n/a	n/a
29	JUN	chr15:39722036-39723003	HUVEC	blood vessel:	n/a	chr15:39722313-39722325 chr15:39722311-39722322 chr15:39722256-39722268
30	RCOR1	chr15:39721963-39722491	GM12878	blood:	n/a	n/a
31	EP300	chr15:39721999-39722791	SK-N-SH	brain:	n/a	chr15:39722128-39722142
32	MTA3	chr15:39721935-39722536	GM12878	blood:	n/a	n/a
33	SIN3AK20	chr15:39721925-39722757	MCF-7	breast:	n/a	n/a
34	PRDM1	chr15:39722160-39722515	Hela-S3	cervix:	n/a	n/a
35	NFIC	chr15:39721916-39722691	SK-N-SH	brain:	n/a	chr15:39722297-39722313
36	CEBPB	chr15:39722114-39722473	MCF-7	breast:	n/a	n/a
37	TCF12	chr15:39721924-39722750	SK-N-SH	brain:	n/a	n/a
38	JUND	chr15:39722021-39722670	SK-N-SH	brain:	n/a	chr15:39722313-39722325 chr15:39722311-39722322 chr15:39722256-39722268
39	CEBPB	chr15:39722223-39722439	Hela-S3	cervix:	n/a	n/a
40	RXRA	chr15:39722015-39722734	SK-N-SH	brain:	n/a	n/a
41	MEF2A	chr15:39721939-39722362	GM12878	blood:	n/a	chr15:39722132-39722140 chr15:39722103-39722124
42	EP300	chr15:39722206-39722478	Hela-S3	cervix:	n/a	n/a
43	NFIC	chr15:39722039-39722505	SK-N-SH	brain:	n/a	chr15:39722297-39722313
44	FOS	chr15:39722261-39722436	MCF10A-Er-Src	breast:	n/a	chr15:39722313-39722325 chr15:39722311-39722322
45	FOS	chr15:39722156-39722468	MCF10A-Er-Src	breast:	n/a	chr15:39722313-39722325 chr15:39722311-39722322 chr15:39722256-39722268
46	FOSL2	chr15:39721993-39722591	SK-N-SH	brain:	n/a	chr15:39722313-39722325 chr15:39722311-39722322 chr15:39722256-39722268
47	RUNX3	chr15:39721963-39722515	GM12878	blood:	n/a	n/a
48	EP300	chr15:39721978-39722672	SK-N-SH	brain:	n/a	chr15:39722128-39722142
49	NFIC	chr15:39721845-39722564	GM12878	blood:	n/a	chr15:39722297-39722313
50	MAX	chr15:39722199-39722589	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:39721051..39725636-chr15:39870055..39875310,7	MCF-7	breast:
2	chr15:39722154..39722685-chr15:39960642..39961199,2	MCF-7	breast:
3	chr15:39721562..39724453-chr15:39734811..39737253,2	MCF-7	breast:
4	chr15:39720867..39723371-chr15:39870394..39874925,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259345	TF binding region
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10459586	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10520130	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070198	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070206	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070207	0.85[ASN][1000 genomes]
rs1158915	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1158916	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1158917	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854059	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854786	0.81[EUR][1000 genomes]
rs11855535	0.81[EUR][1000 genomes]
rs11855543	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11855977	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855990	0.85[ASN][1000 genomes]
rs11857970	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148631	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1551945	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16952151	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16969038	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16969104	0.88[ASN][1000 genomes]
rs3889532	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4286083	0.88[ASN][1000 genomes]
rs4923830	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924362	0.88[ASN][1000 genomes]
rs5028679	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56839831	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56869025	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57248361	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58417285	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59068114	0.85[AMR][1000 genomes]
rs61648928	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171584	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74008128	0.88[AMR][1000 genomes]
rs8025111	0.88[ASN][1000 genomes]
rs8032303	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8034569	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39712600-39724200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:39713200-39727400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:39719200-39723200	Enhancers	Left Ventricle	heart
4	chr15:39719200-39728200	Enhancers	HUVEC	blood vessel
5	chr15:39719400-39723400	Enhancers	Primary hematopoietic stem cells	blood
6	chr15:39719400-39726800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:39719600-39723400	Enhancers	Fetal Thymus	thymus
8	chr15:39719600-39724200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:39719600-39725000	Weak transcription	Right Ventricle	heart
10	chr15:39719600-39727200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr15:39719800-39722400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:39719800-39725000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:39720000-39723800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr15:39720000-39724200	Enhancers	Thymus	Thymus
15	chr15:39720200-39723200	Enhancers	Primary T cells from cord blood	blood
16	chr15:39720200-39723800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:39720200-39723800	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:39720200-39723800	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr15:39720200-39724000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:39720200-39725000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:39720200-39725000	Weak transcription	Fetal Stomach	stomach
22	chr15:39720200-39725600	Weak transcription	Lung	lung
23	chr15:39720200-39726800	Weak transcription	Adipose Nuclei	Adipose
24	chr15:39720400-39722400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:39720400-39724000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:39720400-39726400	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr15:39720800-39722600	Enhancers	Small Intestine	intestine
28	chr15:39721000-39722400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:39721000-39722400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:39721000-39724200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:39721200-39723000	Enhancers	Stomach Mucosa	stomach
32	chr15:39721400-39723200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:39721400-39724000	Enhancers	NH-A	brain
34	chr15:39721600-39722800	Enhancers	Fetal Intestine Large	intestine
35	chr15:39721600-39722800	Enhancers	Hela-S3	cervix
36	chr15:39721600-39724400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:39721600-39724600	Enhancers	Osteobl	bone
38	chr15:39721800-39722600	Enhancers	Primary B cells from cord blood	blood
39	chr15:39721800-39722600	Enhancers	Fetal Heart	heart
40	chr15:39721800-39722600	Flanking Active TSS	GM12878-XiMat	blood
41	chr15:39721800-39722600	Enhancers	K562	blood
42	chr15:39721800-39724400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:39721800-39725400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:39722000-39722400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr15:39722000-39722400	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr15:39722000-39722600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr15:39722000-39722600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr15:39722000-39722800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:39722000-39722800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:39722000-39722800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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