Variant report

Variant	rs11072170
Chromosome Location	chr15:33359370-33359371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:32960265..32963015-chr15:33359103..33361723,2	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
ENSG00000241818	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1026752	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10519781	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[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]
rs10519788	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10775202	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851823	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072175	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072187	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636433	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639303	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]
rs11854308	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs11857866	0.85[JPT][hapmap]
rs12439012	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440002	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592516	0.82[EUR][1000 genomes]
rs17235533	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];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235547	0.83[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]
rs17816711	0.83[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2219156	0.83[EUR][1000 genomes]
rs2219159	0.87[AMR][1000 genomes];0.80[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];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291066	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306278	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]
rs28446831	0.83[EUR][1000 genomes]
rs28510826	0.90[AMR][1000 genomes];0.91[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];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28718544	0.83[ASN][1000 genomes]
rs345794	0.81[ASN][1000 genomes]
rs34606248	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4779604	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779605	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779606	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4780074	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]
rs7167795	0.83[EUR][1000 genomes]
rs8033302	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8039005	0.84[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];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs922510	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]
rs922511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[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
rs11072170	FMN1	cis	Esophagus Mucosa	GTEx
rs11072170	FMN1	cis	Thyroid	GTEx
rs11072170	OCA2	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33348200-33360000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:33355400-33360600	Weak transcription	Right Ventricle	heart
3	chr15:33356600-33359800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr15:33356800-33361000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:33357200-33359800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr15:33357400-33359400	Weak transcription	Fetal Kidney	kidney
7	chr15:33357400-33359600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:33357400-33359600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:33357400-33360200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:33357600-33359400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:33358000-33360600	Active TSS	Colonic Mucosa	Colon
12	chr15:33358200-33359400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:33358200-33359600	Enhancers	HepG2	liver
14	chr15:33358200-33359800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr15:33358200-33359800	Enhancers	Placenta	Placenta
16	chr15:33358200-33360400	Active TSS	Rectal Smooth Muscle	rectum
17	chr15:33358200-33360600	Active TSS	Stomach Mucosa	stomach
18	chr15:33358200-33361000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:33358400-33359400	Enhancers	Fetal Thymus	thymus
20	chr15:33358400-33359600	Enhancers	Hela-S3	cervix
21	chr15:33358400-33359600	Enhancers	NHDF-Ad	bronchial
22	chr15:33358400-33360000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr15:33358400-33360000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr15:33358400-33361800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:33358600-33359600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr15:33358600-33359800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:33358600-33360000	Enhancers	H9 Cell Line	embryonic stem cell
28	chr15:33358600-33360000	Enhancers	Fetal Muscle Leg	muscle
29	chr15:33358600-33360400	Active TSS	Gastric	stomach
30	chr15:33358600-33361800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:33358600-33362000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:33358800-33359600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr15:33358800-33359600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:33358800-33359600	Enhancers	Pancreas	Pancrea
35	chr15:33358800-33359600	Enhancers	HMEC	breast
36	chr15:33358800-33359800	Enhancers	Primary hematopoietic stem cells	blood
37	chr15:33358800-33359800	Enhancers	Esophagus	oesophagus
38	chr15:33358800-33360200	Genic enhancers	NHLF	lung
39	chr15:33358800-33360400	Flanking Active TSS	NH-A	brain
40	chr15:33358800-33361600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:33358800-33361600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr15:33358800-33361600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:33358800-33361800	Enhancers	H1 Cell Line	embryonic stem cell
44	chr15:33358800-33361800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:33358800-33361800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:33359000-33359400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:33359000-33359400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:33359000-33359400	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr15:33359000-33359400	Enhancers	Osteobl	bone
50	chr15:33359000-33359600	Enhancers	HUES48 Cell Line	embryonic stem cell

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