Variant report

Variant	rs8040787
Chromosome Location	chr15:52945210-52945211
allele	A/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	FOXM1	chr15:52945143-52946281	MCF-7	breast:	n/a	n/a
3	MAFK	chr15:52945156-52945541	IMR90	lung:	n/a	n/a
4	SIX5	chr15:52945004-52946253	A549	lung:	n/a	n/a
5	JUND	chr15:52945180-52945568	A549	lung:	n/a	n/a
6	GATA3	chr15:52945044-52947102	MCF-7	breast:	n/a	chr15:52947002-52947023
7	POLR2A	chr15:52945207-52945566	U87	brain:	n/a	n/a
8	NR2F2	chr15:52945038-52946462	MCF-7	breast:	n/a	n/a
9	GATA3	chr15:52944931-52947427	MCF-7	breast:	n/a	chr15:52947002-52947023
10	CEBPB	chr15:52945200-52946422	A549	lung:	n/a	chr15:52946081-52946092 chr15:52946079-52946090
11	HDAC2	chr15:52945094-52946310	MCF-7	breast:	n/a	n/a
12	FOXA2	chr15:52945178-52946382	A549	lung:	n/a	n/a
13	POLR2A	chr15:52945074-52945602	PANC-1	pancreas:	n/a	n/a
14	GATA3	chr15:52944974-52946507	A549	lung:	n/a	n/a
15	TCF7L2	chr15:52945163-52945606	PANC-1	pancreas:	n/a	n/a
16	SP1	chr15:52945003-52946302	A549	lung:	n/a	n/a
17	MXI1	chr15:52944847-52946149	IMR90	lung:	n/a	n/a
18	ELF1	chr15:52945117-52946405	MCF-7	breast:	n/a	chr15:52945334-52945346 chr15:52945583-52945594 chr15:52945583-52945594
19	NR2F2	chr15:52945036-52946336	MCF-7	breast:	n/a	n/a
20	FOSL2	chr15:52945143-52946264	MCF-7	breast:	n/a	chr15:52946149-52946158
21	EP300	chr15:52945137-52946275	MCF-7	breast:	n/a	chr15:52946146-52946160
22	MAX	chr15:52945162-52946260	A549	lung:	n/a	n/a
23	MAX	chr15:52945107-52946212	MCF-7	breast:	n/a	n/a
24	MXI1	chr15:52945203-52946043	Hela-S3	cervix:	n/a	n/a
25	KAP1	chr15:52945076-52946045	HEK293	kidney:	n/a	n/a
26	SP1	chr15:52945098-52946373	A549	lung:	n/a	n/a
27	EP300	chr15:52943398-52945954	SK-N-SH	brain:	n/a	chr15:52944373-52944383 chr15:52943881-52943891 chr15:52943819-52943833
28	FOXA2	chr15:52945057-52946486	A549	lung:	n/a	n/a
29	CEBPB	chr15:52945123-52946399	MCF-7	breast:	n/a	chr15:52946081-52946092 chr15:52946079-52946090
30	SIN3AK20	chr15:52945032-52946247	MCF-7	breast:	n/a	n/a
31	FOSL2	chr15:52945009-52946319	A549	lung:	n/a	chr15:52946149-52946158
32	REST	chr15:52945094-52946273	A549	lung:	n/a	n/a
33	KAP1	chr15:52945208-52945966	U2OS	brain:	n/a	n/a
34	EP300	chr15:52945166-52946393	A549	lung:	n/a	chr15:52946146-52946160
35	GATA3	chr15:52945201-52946260	A549	lung:	n/a	n/a
36	EP300	chr15:52944952-52946439	A549	lung:	n/a	chr15:52946146-52946160
37	FOXM1	chr15:52945150-52946304	MCF-7	breast:	n/a	n/a
38	MAX	chr15:52945046-52946260	A549	lung:	n/a	n/a
39	TCF12	chr15:52944917-52946398	A549	lung:	n/a	chr15:52945948-52945957

No.	Distal block	Cell Line	Cell type
1	chr15:52917289..52919224-chr15:52944457..52946424,2	MCF-7	breast:
2	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:
3	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: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10775148	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10775149	0.82[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070904	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs11070910	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11629479	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11634879	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12102061	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12900462	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs12908944	0.85[EUR][1000 genomes]
rs12916276	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12916405	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2414162	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2414164	0.95[TSI][hapmap]
rs2414165	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2414168	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414169	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414170	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414171	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414174	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2414176	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414177	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2899493	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34340005	0.85[EUR][1000 genomes]
rs35756938	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35760898	0.90[EUR][1000 genomes]
rs4386077	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4404000	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4774635	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4776064	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62025584	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62025586	1.00[EUR][1000 genomes]
rs6493570	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7162184	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7166478	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7168045	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7169849	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7179310	1.00[CEU][hapmap]
rs8026304	0.83[AMR][1000 genomes]
rs8026469	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8032889	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8035115	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8036671	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8036680	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8042646	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs933858	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs933859	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9806267	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][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:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
2	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:52903600-52945400	Weak transcription	Colonic Mucosa	Colon
4	chr15:52904000-52945400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:52904000-52956800	Weak transcription	Esophagus	oesophagus
6	chr15:52908600-52956200	Weak transcription	Gastric	stomach
7	chr15:52909600-52950800	Weak transcription	Pancreas	Pancrea
8	chr15:52927800-52947600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:52927800-52958600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:52928000-52955200	Weak transcription	Thymus	Thymus
11	chr15:52928000-52956400	Weak transcription	Lung	lung
12	chr15:52928200-52945400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:52938000-52945600	Weak transcription	Placenta	Placenta
14	chr15:52938800-52945800	Weak transcription	Psoas Muscle	Psoas
15	chr15:52939600-52945400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:52940200-52945400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr15:52943400-52946000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:52943600-52946000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:52943800-52946000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:52944000-52945800	Genic enhancers	Primary T cells from cord blood	blood
21	chr15:52944000-52946000	Enhancers	Stomach Mucosa	stomach
22	chr15:52944200-52945800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:52944200-52946000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr15:52944200-52946000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:52944200-52946000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr15:52944200-52946200	Enhancers	Colon Smooth Muscle	Colon
27	chr15:52944200-52946400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:52944200-52946400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr15:52944200-52946800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:52944200-52951800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr15:52944200-52965800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:52944400-52945400	Weak transcription	Fetal Muscle Leg	muscle
33	chr15:52944400-52945400	Weak transcription	GM12878-XiMat	blood
34	chr15:52944400-52945400	Enhancers	NHEK	skin
35	chr15:52944400-52945600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:52944400-52945800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr15:52944400-52946000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr15:52944400-52946000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:52944400-52946000	Flanking Active TSS	A549	lung
40	chr15:52944400-52946200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr15:52944400-52946800	Enhancers	HSMM	muscle
42	chr15:52944400-52950000	Weak transcription	Ovary	ovary
43	chr15:52944400-52950400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr15:52944400-52951000	Weak transcription	Fetal Stomach	stomach
45	chr15:52944400-52957000	Weak transcription	Brain Germinal Matrix	brain
46	chr15:52944400-52969600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:52944400-52970200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:52944600-52945400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:52944600-52945400	Enhancers	Fetal Lung	lung
50	chr15:52944600-52945600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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