Variant report

Variant	rs11639303
Chromosome Location	chr15:33360483-33360484
allele	A/C/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	USF2	chr15:33360157-33360636	Hela-S3	cervix:	n/a	n/a
2	MAX	chr15:33360451-33361305	Hela-S3	cervix:	n/a	n/a
3	MAFK	chr15:33360378-33360932	H1-hESC	embryonic stem cell:	n/a	chr15:33360538-33360553 chr15:33360539-33360559 chr15:33360539-33360550 chr15:33360538-33360549 chr15:33360538-33360549
4	MAFK	chr15:33360052-33361252	Hela-S3	cervix:	n/a	chr15:33360538-33360553 chr15:33360539-33360559 chr15:33360539-33360550 chr15:33360538-33360549 chr15:33360538-33360549
5	TEAD4	chr15:33360380-33361450	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr15:33360333-33361523	ECC-1	luminal epithelium:	n/a	n/a
7	FOXA1	chr15:33360018-33360571	T-47D	breast:	n/a	n/a
8	GTF2F1	chr15:33359878-33360559	Hela-S3	cervix:	n/a	n/a
9	ESR1	chr15:33360070-33361318	ECC-1	luminal epithelium:	n/a	chr15:33360240-33360257 chr15:33360423-33360440 chr15:33360241-33360258 chr15:33360241-33360256
10	POLR2A	chr15:33360218-33360622	HepG2	liver:	n/a	n/a
11	GATA3	chr15:33359873-33361562	MCF-7	breast:	n/a	n/a
12	POLR2A	chr15:33360057-33361281	MCF10A-Er-Src	breast:	n/a	n/a
13	TCF12	chr15:33359861-33361393	MCF-7	breast:	n/a	n/a
14	FOXM1	chr15:33360325-33361524	ECC-1	luminal epithelium:	n/a	n/a
15	MAFK	chr15:33360435-33360607	K562	blood:	n/a	chr15:33360538-33360553 chr15:33360539-33360559 chr15:33360539-33360550 chr15:33360538-33360549 chr15:33360538-33360549
16	TCF12	chr15:33359545-33361550	ECC-1	luminal epithelium:	n/a	n/a
17	GABPA	chr15:33359981-33360505	MCF-7	breast:	n/a	n/a
18	REST	chr15:33360431-33361238	A549	lung:	n/a	n/a
19	ESR1	chr15:33359853-33361746	T-47D	breast:	n/a	chr15:33360240-33360257 chr15:33360423-33360440 chr15:33360241-33360258 chr15:33360241-33360256
20	EP300	chr15:33359635-33361383	ECC-1	luminal epithelium:	n/a	chr15:33361205-33361212 chr15:33361033-33361043 chr15:33360216-33360226
21	TEAD4	chr15:33360314-33361486	ECC-1	luminal epithelium:	n/a	n/a
22	TCF7L2	chr15:33360080-33361554	Hela-S3	cervix:	n/a	chr15:33361423-33361433
23	MAX	chr15:33359584-33361558	ECC-1	luminal epithelium:	n/a	chr15:33360283-33360292
24	POLR2A	chr15:33358746-33361577	MCF-7	breast:	n/a	n/a
25	TBP	chr15:33360474-33360679	HepG2	liver:	n/a	n/a
26	MYC	chr15:33360397-33360597	MCF10A-Er-Src	breast:	n/a	n/a
27	SIN3AK20	chr15:33359576-33361559	MCF-7	breast:	n/a	n/a
28	POLR2A	chr15:33360159-33361145	MCF10A-Er-Src	breast:	n/a	n/a
29	MAFK	chr15:33360360-33360724	IMR90	lung:	n/a	chr15:33360538-33360553 chr15:33360539-33360559 chr15:33360539-33360550 chr15:33360538-33360549 chr15:33360538-33360549
30	ELF1	chr15:33360043-33361496	MCF-7	breast:	n/a	chr15:33360256-33360267
31	EP300	chr15:33359476-33361657	ECC-1	luminal epithelium:	n/a	chr15:33361205-33361212 chr15:33361033-33361043 chr15:33360216-33360226
32	ESR1	chr15:33359688-33361370	ECC-1	luminal epithelium:	n/a	chr15:33360240-33360257 chr15:33360423-33360440 chr15:33360241-33360258 chr15:33360241-33360256
33	KAP1	chr15:33360191-33360930	U2OS	brain:	n/a	n/a
34	CTCF	chr15:33360460-33360610	AG04449	skin:	n/a	chr15:33360490-33360499
35	ZNF217	chr15:33359904-33361712	MCF-7	breast:	n/a	n/a
36	POLR2A	chr15:33359330-33360638	SK-N-SH	brain:	n/a	n/a
37	SIN3AK20	chr15:33359910-33361364	MCF-7	breast:	n/a	n/a
38	ESR1	chr15:33360024-33361350	ECC-1	luminal epithelium:	n/a	chr15:33360240-33360257 chr15:33360423-33360440 chr15:33360241-33360258 chr15:33360241-33360256
39	MAFK	chr15:33360360-33360726	HepG2	liver:	n/a	chr15:33360538-33360553 chr15:33360539-33360559 chr15:33360539-33360550 chr15:33360538-33360549 chr15:33360538-33360549
40	ESR1	chr15:33359875-33361853	T-47D	breast:	n/a	chr15:33360240-33360257 chr15:33360423-33360440 chr15:33360241-33360258 chr15:33360241-33360256
41	POLR2A	chr15:33360021-33360676	U87	brain:	n/a	n/a
42	FOXM1	chr15:33360364-33361500	ECC-1	luminal epithelium:	n/a	n/a
43	TAF1	chr15:33360084-33360684	ECC-1	luminal epithelium:	n/a	n/a
44	NR2F2	chr15:33359931-33361318	MCF-7	breast:	n/a	n/a
45	ELF1	chr15:33360085-33360617	HepG2	liver:	n/a	chr15:33360256-33360267
46	POLR2A	chr15:33360178-33360687	U87	brain:	n/a	n/a
47	POLR2A	chr15:33360058-33360601	MCF-7	breast:	n/a	n/a
48	POLR2A	chr15:33360051-33361316	ECC-1	luminal epithelium:	n/a	n/a
49	ESR1	chr15:33359786-33361435	T-47D	breast:	n/a	chr15:33360240-33360257 chr15:33360423-33360440 chr15:33360241-33360258 chr15:33360241-33360256
50	POLR2A	chr15:33360178-33360727	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:33360408..33362379-chr15:33362981..33365485,2	MCF-7	breast:
2	chr15:32960265..32963015-chr15:33359103..33361723,2	MCF-7	breast:
3	chr15:33360297..33360858-chr2:122288120..122289062,2	Hela-S3	cervix:
4	chr15:33359729..33362501-chr7:80547999..80549877,2	MCF-7	breast:
5	chr15:33297830..33309224-chr15:33355310..33362883,25	MCF-7	breast:

Variant related genes	Relation type
FMN1	TF binding region
ENSG00000241818	Chromatin interaction
ENSG00000264229	Chromatin interaction
ENSG00000259686	Chromatin interaction
ENSG00000075223	Chromatin interaction
ENSG00000074054	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1026752	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10519781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519788	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10775202	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072170	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072187	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636433	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857866	0.85[JPT][hapmap]
rs12439012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440002	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235533	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17816711	0.91[CEU][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2219159	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2291064	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291065	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291066	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306278	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510826	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28551066	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28576977	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28603193	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28718544	0.83[ASN][1000 genomes]
rs345794	0.81[ASN][1000 genomes]
rs34606248	0.81[ASN][1000 genomes]
rs4779604	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779605	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779606	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4780074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033302	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8039005	0.92[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs922510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs922511	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv524708	chr15:33357262-33365334	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11639303	FMN1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33355400-33360600	Weak transcription	Right Ventricle	heart
2	chr15:33356800-33361000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:33358000-33360600	Active TSS	Colonic Mucosa	Colon
4	chr15:33358200-33360600	Active TSS	Stomach Mucosa	stomach
5	chr15:33358200-33361000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:33358400-33361800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:33358600-33361800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:33358600-33362000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:33358800-33361600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:33358800-33361600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr15:33358800-33361600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:33358800-33361800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr15:33358800-33361800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:33358800-33361800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:33359000-33360600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:33359000-33361400	Flanking Active TSS	HSMMtube	muscle
17	chr15:33359200-33361000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr15:33359200-33361000	Flanking Active TSS	HSMM	muscle
19	chr15:33359200-33361400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:33359400-33360800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:33359400-33360800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:33359400-33360800	Flanking Active TSS	Osteobl	bone
23	chr15:33359400-33361000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr15:33359400-33361000	Flanking Active TSS	Fetal Thymus	thymus
25	chr15:33359400-33361600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:33359400-33361800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:33359400-33361800	Enhancers	Fetal Kidney	kidney
28	chr15:33359600-33360600	Active TSS	Pancreas	Pancrea
29	chr15:33359600-33360600	Flanking Active TSS	NHDF-Ad	bronchial
30	chr15:33359600-33360800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr15:33359600-33361000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr15:33359600-33361000	Enhancers	Spleen	Spleen
33	chr15:33359600-33361000	Flanking Active TSS	NHEK	skin
34	chr15:33359600-33361200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:33359600-33361200	Flanking Active TSS	HMEC	breast
36	chr15:33359600-33361400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:33359600-33361400	Flanking Active TSS	Hela-S3	cervix
38	chr15:33359600-33361600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr15:33359600-33361600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:33359800-33360600	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr15:33359800-33360600	Active TSS	Duodenum Mucosa	Duodenum
42	chr15:33359800-33360600	Flanking Active TSS	Placenta	Placenta
43	chr15:33359800-33360800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr15:33359800-33360800	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr15:33359800-33360800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:33359800-33361000	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr15:33359800-33361000	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr15:33359800-33361200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:33359800-33361200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr15:33359800-33361400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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