Variant report

Variant	rs922510
Chromosome Location	chr15:33361642-33361643
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	EP300	chr15:33361416-33361842	T-47D	breast:	n/a	n/a
2	STAT3	chr15:33361481-33361765	MCF10A-Er-Src	breast:	n/a	n/a
3	ESR1	chr15:33359853-33361746	T-47D	breast:	n/a	chr15:33360240-33360257 chr15:33360423-33360440 chr15:33360241-33360258 chr15:33360241-33360256
4	EP300	chr15:33359476-33361657	ECC-1	luminal epithelium:	n/a	chr15:33361205-33361212 chr15:33361033-33361043 chr15:33360216-33360226
5	ESR1	chr15:33361438-33361879	T-47D	breast:	n/a	n/a
6	ZNF217	chr15:33359904-33361712	MCF-7	breast:	n/a	n/a
7	GATA3	chr15:33360728-33361834	T-47D	breast:	n/a	n/a
8	ESR1	chr15:33359875-33361853	T-47D	breast:	n/a	chr15:33360240-33360257 chr15:33360423-33360440 chr15:33360241-33360258 chr15:33360241-33360256
9	ESR1	chr15:33361454-33361773	T-47D	breast:	n/a	n/a
10	FOXA1	chr15:33361353-33361728	T-47D	breast:	n/a	n/a
11	NFIC	chr15:33359517-33361695	ECC-1	luminal epithelium:	n/a	n/a
12	GATA3	chr15:33359929-33361814	T-47D	breast:	n/a	n/a
13	ESR1	chr15:33359895-33361858	T-47D	breast:	n/a	chr15:33360240-33360257 chr15:33360423-33360440 chr15:33360241-33360258 chr15:33360241-33360256
14	ESR1	chr15:33359832-33361838	T-47D	breast:	n/a	chr15:33360240-33360257 chr15:33360423-33360440 chr15:33360241-33360258 chr15:33360241-33360256
15	CTCF	chr15:33361600-33361750	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:33298321..33300066-chr15:33361018..33362893,2	MCF-7	breast:
2	chr15:33360408..33362379-chr15:33362981..33365485,2	MCF-7	breast:
3	chr15:32960265..32963015-chr15:33359103..33361723,2	MCF-7	breast:
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
ENSG00000075223	Chromatin interaction
ENSG00000259686	Chromatin interaction
ENSG00000241818	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1026752	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10519781	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519788	0.92[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];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072170	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072187	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636433	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639303	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]
rs11857866	0.85[JPT][hapmap]
rs12439012	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]
rs12440002	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.96[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];0.80[MEX][hapmap];0.82[TSI][hapmap];0.87[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17816711	0.91[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2219159	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2291064	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291065	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291066	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306278	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510826	0.90[AMR][1000 genomes];0.97[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	0.88[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	0.96[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[YRI][hapmap];0.92[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];0.94[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];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033302	0.92[AMR][1000 genomes];0.94[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];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs922511	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs922510	FMN1	cis	Thyroid	GTEx
rs922510	FAN1	cis	parietal	SCAN
rs922510	FMN1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33358400-33361800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:33358600-33361800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:33358600-33362000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:33358800-33361800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr15:33358800-33361800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:33358800-33361800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:33359400-33361800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:33359400-33361800	Enhancers	Fetal Kidney	kidney
9	chr15:33360400-33361800	Enhancers	H9 Cell Line	embryonic stem cell
10	chr15:33360400-33361800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr15:33360400-33361800	Enhancers	Fetal Muscle Leg	muscle
12	chr15:33360400-33361800	Enhancers	NHLF	lung
13	chr15:33360400-33362600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:33360600-33361800	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr15:33360600-33362000	Enhancers	Placenta	Placenta
16	chr15:33360800-33361800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr15:33360800-33362200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr15:33360800-33363000	Enhancers	Stomach Mucosa	stomach
19	chr15:33361000-33361800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr15:33361000-33361800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:33361000-33361800	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr15:33361000-33361800	Enhancers	Fetal Thymus	thymus
23	chr15:33361000-33362000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr15:33361000-33362000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr15:33361000-33362000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr15:33361200-33361800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:33361200-33361800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:33361200-33361800	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr15:33361200-33361800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr15:33361200-33362200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:33361200-33378800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:33361400-33361800	Enhancers	Small Intestine	intestine
33	chr15:33361400-33361800	Enhancers	A549	lung
34	chr15:33361400-33361800	Enhancers	HSMMtube	muscle
35	chr15:33361400-33362000	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr15:33361400-33362000	Enhancers	Thymus	Thymus
37	chr15:33361400-33362000	Enhancers	Hela-S3	cervix
38	chr15:33361400-33362200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr15:33361400-33364600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:33361600-33361800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:33361600-33361800	Weak transcription	Esophagus	oesophagus
42	chr15:33361600-33361800	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr15:33361600-33362200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr15:33361600-33366200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:33361600-33375600	Weak transcription	HSMM	muscle

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