Variant report

Variant	rs4780074
Chromosome Location	chr15:33358079-33358080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:33314218..33314802-chr15:33358026..33358783,2	MCF-7	breast:
2	chr15:33312296..33313936-chr15:33357129..33359638,2	MCF-7	breast:
3	chr15:33297830..33309224-chr15:33355310..33362883,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259686	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1026752	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10519781	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]
rs10519788	0.91[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];0.97[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];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072170	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072187	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636433	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639303	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]
rs11854308	0.85[CEU][hapmap]
rs12439012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[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];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235533	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235547	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]
rs17816711	0.92[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2219159	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2291064	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291065	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291066	0.88[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];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510826	0.89[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	0.89[AMR][1000 genomes];0.88[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	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779605	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779606	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]
rs8033302	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8039005	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs922510	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]
rs922511	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4780074	FMN1	cis	Esophagus Mucosa	GTEx
rs4780074	FMN1	cis	Thyroid	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33345600-33358200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:33348000-33358200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:33348200-33360000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:33350400-33358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:33350400-33358800	Weak transcription	Pancreas	Pancrea
6	chr15:33350600-33358200	Weak transcription	Placenta	Placenta
7	chr15:33355000-33358600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:33355400-33360600	Weak transcription	Right Ventricle	heart
9	chr15:33355600-33358600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:33355600-33358800	Weak transcription	Small Intestine	intestine
11	chr15:33355600-33358800	Active TSS	Thymus	Thymus
12	chr15:33355800-33358600	Weak transcription	Gastric	stomach
13	chr15:33356400-33359200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:33356600-33358400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr15:33356600-33359000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:33356600-33359800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr15:33356800-33358200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:33356800-33358400	Weak transcription	Hela-S3	cervix
19	chr15:33356800-33361000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:33357000-33358200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:33357000-33358200	Weak transcription	HepG2	liver
22	chr15:33357000-33359200	Enhancers	Duodenum Mucosa	Duodenum
23	chr15:33357200-33358200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:33357200-33358400	Weak transcription	Fetal Thymus	thymus
25	chr15:33357200-33358800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:33357200-33359200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:33357200-33359800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr15:33357400-33358200	Weak transcription	Stomach Mucosa	stomach
29	chr15:33357400-33358200	Weak transcription	NHLF	lung
30	chr15:33357400-33358400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:33357400-33358400	Weak transcription	NHDF-Ad	bronchial
32	chr15:33357400-33358600	Weak transcription	Lung	lung
33	chr15:33357400-33358800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:33357400-33358800	Weak transcription	Esophagus	oesophagus
35	chr15:33357400-33358800	Weak transcription	HMEC	breast
36	chr15:33357400-33359400	Weak transcription	Fetal Kidney	kidney
37	chr15:33357400-33359600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:33357400-33359600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:33357400-33360200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:33357600-33358200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:33357600-33358200	Enhancers	HSMM	muscle
42	chr15:33357600-33358200	Flanking Active TSS	Osteobl	bone
43	chr15:33357600-33359400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:33357800-33358600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:33357800-33358600	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr15:33357800-33358800	Active TSS	NH-A	brain
47	chr15:33357800-33359200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:33358000-33358200	Enhancers	HSMMtube	muscle
49	chr15:33358000-33358400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:33358000-33358400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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