Variant report

Variant	rs2414167
Chromosome Location	chr15:52907428-52907429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52906245..52907882-chr15:52919782..52921282,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1080731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10851520	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10851521	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11070906	1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11070907	1.00[CHB][hapmap]
rs11070909	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11853917	1.00[CHB][hapmap]
rs11855616	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs11857150	1.00[CHB][hapmap]
rs12594964	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12898644	1.00[CHB][hapmap]
rs12902679	1.00[CHB][hapmap]
rs12914502	1.00[CHB][hapmap]
rs12915981	1.00[CHB][hapmap]
rs13329393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17614559	1.00[CHB][hapmap]
rs1863512	0.89[CHB][hapmap]
rs2288271	1.00[CHB][hapmap]
rs2414160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2414161	1.00[CHB][hapmap]
rs2414163	1.00[CHB][hapmap]
rs2414166	1.00[CHB][hapmap]
rs28368342	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2899492	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3751614	1.00[CHB][hapmap]
rs4390542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4548810	0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs4636853	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4774634	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs4776058	1.00[CHB][hapmap]
rs4776063	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4776065	1.00[CHB][hapmap]
rs4776066	1.00[CHB][hapmap]
rs7167494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73396785	0.82[EUR][1000 genomes]
rs8026800	1.00[CHB][hapmap]
rs8030141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8030871	1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs8036979	1.00[TSI][hapmap]
rs933860	1.00[CHB][hapmap]

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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv457140	chr15:52901433-52968746	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2414167	MYO5A	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52861200-52925200	Weak transcription	Stomach Mucosa	stomach
2	chr15:52861800-52908400	Weak transcription	Gastric	stomach
3	chr15:52861800-52934800	Weak transcription	Right Ventricle	heart
4	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
5	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:52872200-52933800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:52872600-52920800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:52873400-52928000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:52873800-52909600	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr15:52874200-52917000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:52874800-52944200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:52875400-52916200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:52878200-52909600	Strong transcription	Liver	Liver
14	chr15:52882200-52920000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:52882400-52926000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr15:52885600-52945200	Weak transcription	Spleen	Spleen
17	chr15:52891400-52927600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:52891600-52908400	Weak transcription	Aorta	Aorta
19	chr15:52899000-52920400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:52899600-52917000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:52899600-52944400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:52900400-52909600	Strong transcription	Adipose Nuclei	Adipose
23	chr15:52900400-52911800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr15:52900600-52907800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:52900600-52909600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:52900600-52944000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr15:52900800-52945200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:52902200-52943800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:52902400-52908000	Weak transcription	Psoas Muscle	Psoas
30	chr15:52902400-52911000	Weak transcription	A549	lung
31	chr15:52902400-52914200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr15:52902400-52916400	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:52902400-52925200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:52902400-52934800	Weak transcription	NH-A	brain
35	chr15:52902600-52914000	Weak transcription	Lung	lung
36	chr15:52902600-52915800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:52902600-52916400	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:52902600-52927400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:52902600-52942000	Weak transcription	HUVEC	blood vessel
40	chr15:52902800-52916400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:52903000-52911000	Weak transcription	HSMM	muscle
42	chr15:52903400-52925400	Weak transcription	Brain Germinal Matrix	brain
43	chr15:52903400-52933800	Weak transcription	Fetal Heart	heart
44	chr15:52903400-52943800	Weak transcription	Hela-S3	cervix
45	chr15:52903400-52944000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:52903600-52942400	Weak transcription	Dnd41	blood
47	chr15:52903600-52945400	Weak transcription	Colonic Mucosa	Colon
48	chr15:52904000-52908400	Weak transcription	NHDF-Ad	bronchial
49	chr15:52904000-52914600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:52904000-52922800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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