Variant report

Variant	rs17708373
Chromosome Location	chr15:52945458-52945459
allele	C/G
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	RFX5	chr15:52941897-52945775	SK-N-SH	brain:	n/a	chr15:52944270-52944284
2	MAZ	chr15:52945310-52945495	K562	blood:	n/a	n/a
3	FOXM1	chr15:52945143-52946281	MCF-7	breast:	n/a	n/a
4	MAFK	chr15:52945156-52945541	IMR90	lung:	n/a	n/a
5	SIX5	chr15:52945004-52946253	A549	lung:	n/a	n/a
6	MAX	chr15:52945274-52945829	Hela-S3	cervix:	n/a	n/a
7	JUND	chr15:52945180-52945568	A549	lung:	n/a	n/a
8	JUND	chr15:52945281-52945806	K562	blood:	n/a	n/a
9	GABPA	chr15:52945427-52946174	A549	lung:	n/a	n/a
10	GATA3	chr15:52945044-52947102	MCF-7	breast:	n/a	chr15:52947002-52947023
11	POLR2A	chr15:52945207-52945566	U87	brain:	n/a	n/a
12	NR2F2	chr15:52945038-52946462	MCF-7	breast:	n/a	n/a
13	GATA3	chr15:52944931-52947427	MCF-7	breast:	n/a	chr15:52947002-52947023
14	FOS	chr15:52945384-52946036	MCF10A-Er-Src	breast:	n/a	chr15:52945720-52945731
15	GATA3	chr15:52945435-52946288	T-47D	breast:	n/a	n/a
16	BHLHE40	chr15:52945318-52945486	K562	blood:	n/a	chr15:52945333-52945349
17	TFAP2A	chr15:52945377-52945880	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr15:52945200-52946422	A549	lung:	n/a	chr15:52946081-52946092 chr15:52946079-52946090
19	HDAC2	chr15:52945094-52946310	MCF-7	breast:	n/a	n/a
20	MYC	chr15:52945237-52946135	MCF10A-Er-Src	breast:	n/a	n/a
21	NFIC	chr15:52945411-52946087	ECC-1	luminal epithelium:	n/a	n/a
22	FOS	chr15:52945432-52945909	HUVEC	blood vessel:	n/a	chr15:52945720-52945731
23	FOS	chr15:52945234-52946222	MCF10A-Er-Src	breast:	n/a	chr15:52946149-52946158 chr15:52945720-52945731
24	TFAP2C	chr15:52945272-52945910	Hela-S3	cervix:	n/a	n/a
25	RCOR1	chr15:52945248-52945532	K562	blood:	n/a	n/a
26	FOXA2	chr15:52945178-52946382	A549	lung:	n/a	n/a
27	POLR2A	chr15:52945074-52945602	PANC-1	pancreas:	n/a	n/a
28	GATA3	chr15:52944974-52946507	A549	lung:	n/a	n/a
29	NR3C1	chr15:52945455-52946011	A549	lung:	n/a	n/a
30	TCF7L2	chr15:52945163-52945606	PANC-1	pancreas:	n/a	n/a
31	SP1	chr15:52945003-52946302	A549	lung:	n/a	n/a
32	MXI1	chr15:52944847-52946149	IMR90	lung:	n/a	n/a
33	ELF1	chr15:52945117-52946405	MCF-7	breast:	n/a	chr15:52945334-52945346 chr15:52945583-52945594 chr15:52945583-52945594
34	SIN3AK20	chr15:52945267-52945856	PFSK-1	brain:	n/a	n/a
35	NR2F2	chr15:52945036-52946336	MCF-7	breast:	n/a	n/a
36	FOSL2	chr15:52945143-52946264	MCF-7	breast:	n/a	chr15:52946149-52946158
37	EP300	chr15:52945137-52946275	MCF-7	breast:	n/a	chr15:52946146-52946160
38	MAX	chr15:52945162-52946260	A549	lung:	n/a	n/a
39	MAX	chr15:52945107-52946212	MCF-7	breast:	n/a	n/a
40	MXI1	chr15:52945203-52946043	Hela-S3	cervix:	n/a	n/a
41	KAP1	chr15:52945076-52946045	HEK293	kidney:	n/a	n/a
42	MYC	chr15:52945310-52945908	MCF10A-Er-Src	breast:	n/a	n/a
43	MYC	chr15:52945372-52945530	K562	blood:	n/a	n/a
44	SP1	chr15:52945098-52946373	A549	lung:	n/a	n/a
45	STAT3	chr15:52945364-52946020	MCF10A-Er-Src	breast:	n/a	n/a
46	EP300	chr15:52943398-52945954	SK-N-SH	brain:	n/a	chr15:52944373-52944383 chr15:52943881-52943891 chr15:52943819-52943833
47	FOXA2	chr15:52945057-52946486	A549	lung:	n/a	n/a
48	CEBPB	chr15:52945123-52946399	MCF-7	breast:	n/a	chr15:52946081-52946092 chr15:52946079-52946090
49	SIN3AK20	chr15:52945032-52946247	MCF-7	breast:	n/a	n/a
50	FOSL2	chr15:52945009-52946319	A549	lung:	n/a	chr15:52946149-52946158

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	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:
4	chr15:52580472..52581982-chr15:52945123..52947114,2	MCF-7	breast:

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

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17651844	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs17651850	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap]
rs2414172	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35689765	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3751613	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57141956	0.95[EUR][1000 genomes]
rs59336405	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59360599	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59808396	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59920981	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59997215	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60200908	1.00[EUR][1000 genomes]
rs61021982	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7182896	1.00[EUR][1000 genomes]
rs72623993	1.00[EUR][1000 genomes]
rs72623994	1.00[EUR][1000 genomes]
rs72623995	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72623996	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72623997	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72623998	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72623999	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72624000	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs877974	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs877975	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs933861	0.80[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:116 , 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	chr15:52938000-52945600	Weak transcription	Placenta	Placenta
10	chr15:52938800-52945800	Weak transcription	Psoas Muscle	Psoas
11	chr15:52943400-52946000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:52943600-52946000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:52943800-52946000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:52944000-52945800	Genic enhancers	Primary T cells from cord blood	blood
15	chr15:52944000-52946000	Enhancers	Stomach Mucosa	stomach
16	chr15:52944200-52945800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:52944200-52946000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr15:52944200-52946000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:52944200-52946000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
20	chr15:52944200-52946200	Enhancers	Colon Smooth Muscle	Colon
21	chr15:52944200-52946400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:52944200-52946400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:52944200-52946800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:52944200-52951800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr15:52944200-52965800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:52944400-52945600	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:52944400-52945800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr15:52944400-52946000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr15:52944400-52946000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:52944400-52946000	Flanking Active TSS	A549	lung
31	chr15:52944400-52946200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr15:52944400-52946800	Enhancers	HSMM	muscle
33	chr15:52944400-52950000	Weak transcription	Ovary	ovary
34	chr15:52944400-52950400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:52944400-52951000	Weak transcription	Fetal Stomach	stomach
36	chr15:52944400-52957000	Weak transcription	Brain Germinal Matrix	brain
37	chr15:52944400-52969600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:52944400-52970200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:52944600-52945600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:52944600-52945600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:52944600-52945600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr15:52944600-52945600	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr15:52944600-52945600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr15:52944600-52945800	Enhancers	Brain Cingulate Gyrus	brain
45	chr15:52944600-52945800	Enhancers	Brain Hippocampus Middle	brain
46	chr15:52944600-52945800	Enhancers	Fetal Intestine Small	intestine
47	chr15:52944600-52946000	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr15:52944600-52946000	Enhancers	Brain Anterior Caudate	brain
49	chr15:52944600-52946000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr15:52944600-52946000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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