Variant report

Variant	rs2306278
Chromosome Location	chr15:33356935-33356936
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:33297830..33309224-chr15:33355310..33362883,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259686	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1026752	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10519781	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]
rs10519788	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10775202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851823	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072170	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072175	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072187	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636433	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639303	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]
rs11854308	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12439012	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592516	0.81[EUR][1000 genomes]
rs17235533	0.88[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]
rs17235547	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]
rs17816711	0.96[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2219156	0.82[EUR][1000 genomes]
rs2219159	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2291064	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291065	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291066	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28446831	0.81[EUR][1000 genomes]
rs28510826	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28551066	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28576977	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28603193	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28718544	0.83[ASN][1000 genomes]
rs345794	0.81[ASN][1000 genomes]
rs34606248	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4779604	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779606	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]
rs4780074	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]
rs7167795	0.82[EUR][1000 genomes]
rs8033302	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8039005	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs922510	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]
rs922511	0.88[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]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2306278	FMN1	cis	Esophagus Mucosa	GTEx
rs2306278	FMN1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33337000-33358000	Weak transcription	Colonic Mucosa	Colon
2	chr15:33345600-33358200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:33348000-33358200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr15:33348200-33360000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:33350400-33358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:33350400-33358800	Weak transcription	Pancreas	Pancrea
7	chr15:33350600-33358200	Weak transcription	Placenta	Placenta
8	chr15:33355000-33358600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:33355400-33360600	Weak transcription	Right Ventricle	heart
10	chr15:33355600-33358600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:33355600-33358800	Weak transcription	Small Intestine	intestine
12	chr15:33355600-33358800	Active TSS	Thymus	Thymus
13	chr15:33355800-33358600	Weak transcription	Gastric	stomach
14	chr15:33356000-33357600	Genic enhancers	HSMM	muscle
15	chr15:33356200-33357400	Enhancers	Fetal Kidney	kidney
16	chr15:33356200-33357400	Enhancers	NHDF-Ad	bronchial
17	chr15:33356400-33357000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr15:33356400-33357400	Flanking Active TSS	Osteobl	bone
19	chr15:33356400-33357800	Flanking Active TSS	NH-A	brain
20	chr15:33356400-33359200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:33356600-33357000	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr15:33356600-33357000	Flanking Active TSS	NHLF	lung
23	chr15:33356600-33357200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr15:33356600-33357400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:33356600-33357400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:33356600-33357400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr15:33356600-33357400	Active TSS	Stomach Mucosa	stomach
28	chr15:33356600-33358400	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr15:33356600-33359000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:33356600-33359800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr15:33356800-33357000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr15:33356800-33357000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:33356800-33357000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:33356800-33357000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:33356800-33357000	Enhancers	HepG2	liver
36	chr15:33356800-33357000	Flanking Active TSS	HSMMtube	muscle
37	chr15:33356800-33357200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:33356800-33357200	Enhancers	Fetal Thymus	thymus
39	chr15:33356800-33357200	Active TSS	Rectal Smooth Muscle	rectum
40	chr15:33356800-33357400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:33356800-33357400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:33356800-33357400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:33356800-33357400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:33356800-33357400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:33356800-33357400	Enhancers	Esophagus	oesophagus
46	chr15:33356800-33357400	Active TSS	Lung	lung
47	chr15:33356800-33357400	Enhancers	HMEC	breast
48	chr15:33356800-33357600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:33356800-33357600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr15:33356800-33358000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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