Variant report

Variant	rs73398904
Chromosome Location	chr15:52946055-52946056
allele	G/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	NR3C1	chr15:52945759-52946178	A549	lung:	n/a	n/a
2	FOXM1	chr15:52945143-52946281	MCF-7	breast:	n/a	n/a
3	JUND	chr15:52945474-52946274	MCF-7	breast:	n/a	chr15:52946149-52946158
4	SIX5	chr15:52945004-52946253	A549	lung:	n/a	n/a
5	GATA3	chr15:52945833-52946189	T-47D	breast:	n/a	n/a
6	FOSL2	chr15:52945593-52946196	A549	lung:	n/a	chr15:52946149-52946158
7	ESR1	chr15:52945907-52946167	T-47D	breast:	n/a	n/a
8	CEBPB	chr15:52945936-52946254	HepG2	liver:	n/a	chr15:52946081-52946092 chr15:52946079-52946090
9	GABPA	chr15:52945427-52946174	A549	lung:	n/a	n/a
10	CEBPB	chr15:52945536-52946375	MCF-7	breast:	n/a	chr15:52946081-52946092 chr15:52946079-52946090
11	CEBPB	chr15:52945576-52946254	Hela-S3	cervix:	n/a	chr15:52946081-52946092 chr15:52946079-52946090
12	GATA3	chr15:52945044-52947102	MCF-7	breast:	n/a	chr15:52947002-52947023
13	NR2F2	chr15:52945038-52946462	MCF-7	breast:	n/a	n/a
14	GATA3	chr15:52944931-52947427	MCF-7	breast:	n/a	chr15:52947002-52947023
15	GATA3	chr15:52945435-52946288	T-47D	breast:	n/a	n/a
16	CEBPB	chr15:52945200-52946422	A549	lung:	n/a	chr15:52946081-52946092 chr15:52946079-52946090
17	HDAC2	chr15:52945094-52946310	MCF-7	breast:	n/a	n/a
18	NR3C1	chr15:52945510-52946155	A549	lung:	n/a	n/a
19	MYC	chr15:52945237-52946135	MCF10A-Er-Src	breast:	n/a	n/a
20	NFIC	chr15:52945411-52946087	ECC-1	luminal epithelium:	n/a	n/a
21	CEBPB	chr15:52945486-52946271	A549	lung:	n/a	chr15:52946081-52946092 chr15:52946079-52946090
22	FOS	chr15:52945234-52946222	MCF10A-Er-Src	breast:	n/a	chr15:52946149-52946158 chr15:52945720-52945731
23	JUND	chr15:52945581-52946257	A549	lung:	n/a	chr15:52946149-52946158
24	ZBTB33	chr15:52945595-52946172	A549	lung:	n/a	n/a
25	FOXA2	chr15:52945178-52946382	A549	lung:	n/a	n/a
26	GATA3	chr15:52944974-52946507	A549	lung:	n/a	n/a
27	SP1	chr15:52945003-52946302	A549	lung:	n/a	n/a
28	NR3C1	chr15:52945588-52946147	A549	lung:	n/a	n/a
29	MXI1	chr15:52944847-52946149	IMR90	lung:	n/a	n/a
30	JUND	chr15:52945489-52946463	MCF-7	breast:	n/a	chr15:52946149-52946158
31	ELF1	chr15:52945117-52946405	MCF-7	breast:	n/a	chr15:52945334-52945346 chr15:52945583-52945594 chr15:52945583-52945594
32	NR2F2	chr15:52945036-52946336	MCF-7	breast:	n/a	n/a
33	FOSL2	chr15:52945143-52946264	MCF-7	breast:	n/a	chr15:52946149-52946158
34	ESR1	chr15:52945924-52946213	T-47D	breast:	n/a	n/a
35	REST	chr15:52945706-52946328	MCF-7	breast:	n/a	n/a
36	EP300	chr15:52945137-52946275	MCF-7	breast:	n/a	chr15:52946146-52946160
37	MAX	chr15:52945162-52946260	A549	lung:	n/a	n/a
38	MAX	chr15:52945107-52946212	MCF-7	breast:	n/a	n/a
39	FOXA1	chr15:52945776-52946124	T-47D	breast:	n/a	n/a
40	FOXA1	chr15:52945741-52946227	T-47D	breast:	n/a	n/a
41	ZNF217	chr15:52945508-52946229	MCF-7	breast:	n/a	n/a
42	SP1	chr15:52945098-52946373	A549	lung:	n/a	n/a
43	FOXA2	chr15:52945057-52946486	A549	lung:	n/a	n/a
44	CEBPB	chr15:52945123-52946399	MCF-7	breast:	n/a	chr15:52946081-52946092 chr15:52946079-52946090
45	SIN3AK20	chr15:52945032-52946247	MCF-7	breast:	n/a	n/a
46	FOS	chr15:52945564-52946173	MCF10A-Er-Src	breast:	n/a	chr15:52946149-52946158 chr15:52945720-52945731
47	FOSL2	chr15:52945009-52946319	A549	lung:	n/a	chr15:52946149-52946158
48	ELF1	chr15:52945452-52946075	A549	lung:	n/a	chr15:52945583-52945594 chr15:52945583-52945594
49	TCF12	chr15:52945571-52946212	A549	lung:	n/a	chr15:52945948-52945957
50	GATA3	chr15:52945991-52946275	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52945439..52946381-chr15:52970859..52971765,2	MCF-7	breast:
2	chr15:52917289..52919224-chr15:52944457..52946424,2	MCF-7	breast:
3	chr15:52310236..52311832-chr15:52945578..52947568,2	MCF-7	breast:
4	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:
5	chr15:52580472..52581982-chr15:52945123..52947114,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259935	TF binding region
FAM214A	TF binding region
ENSG00000069956	Chromatin interaction
ENSG00000047346	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10851522	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12438599	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12595161	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17651917	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1991300	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73396772	0.89[ASN][1000 genomes]
rs8026277	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS 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	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv457140	chr15:52901433-52968746	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr15:52904000-52956800	Weak transcription	Esophagus	oesophagus
3	chr15:52908600-52956200	Weak transcription	Gastric	stomach
4	chr15:52909600-52950800	Weak transcription	Pancreas	Pancrea
5	chr15:52927800-52947600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr15:52927800-52958600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:52928000-52955200	Weak transcription	Thymus	Thymus
8	chr15:52928000-52956400	Weak transcription	Lung	lung
9	chr15:52944200-52946200	Enhancers	Colon Smooth Muscle	Colon
10	chr15:52944200-52946400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:52944200-52946400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:52944200-52946800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:52944200-52951800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr15:52944200-52965800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr15:52944400-52946200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr15:52944400-52946800	Enhancers	HSMM	muscle
17	chr15:52944400-52950000	Weak transcription	Ovary	ovary
18	chr15:52944400-52950400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr15:52944400-52951000	Weak transcription	Fetal Stomach	stomach
20	chr15:52944400-52957000	Weak transcription	Brain Germinal Matrix	brain
21	chr15:52944400-52969600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:52944400-52970200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:52944600-52946200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr15:52944600-52946200	Enhancers	HSMMtube	muscle
25	chr15:52944600-52947600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:52944600-52947800	Enhancers	HMEC	breast
27	chr15:52944600-52947800	Enhancers	NHLF	lung
28	chr15:52944600-52948400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:52944600-52949600	Weak transcription	Fetal Brain Female	brain
30	chr15:52944600-52950000	Enhancers	Liver	Liver
31	chr15:52944600-52962000	Weak transcription	Aorta	Aorta
32	chr15:52944600-52965000	Strong transcription	Primary B cells from cord blood	blood
33	chr15:52944600-52965400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr15:52944600-52969800	Weak transcription	Fetal Brain Male	brain
35	chr15:52944800-52951000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:52944800-52952000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr15:52945000-52948200	Strong transcription	Fetal Thymus	thymus
38	chr15:52945000-52965400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:52945000-52968600	Weak transcription	HepG2	liver
40	chr15:52945200-52946200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr15:52945200-52946200	Genic enhancers	HUVEC	blood vessel
42	chr15:52945200-52947000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:52945200-52948200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr15:52945200-52948200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:52945200-52950600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr15:52945200-52959800	Weak transcription	Dnd41	blood
47	chr15:52945400-52946200	Enhancers	NHDF-Ad	bronchial
48	chr15:52945400-52946800	Strong transcription	GM12878-XiMat	blood
49	chr15:52945400-52951200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:52945400-52951600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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