Variant report

Variant	rs8040558
Chromosome Location	chr15:52614149-52614150
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	chr15:52600034..52602516-chr15:52612985..52614649,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10518683	0.81[ASW][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1104800	0.88[ASN][1000 genomes]
rs1108808	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11856942	1.00[CEU][hapmap]
rs12101973	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12913979	0.88[ASN][1000 genomes]
rs13329278	0.81[ASW][hapmap];0.81[LWK][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13329402	0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13329500	0.81[ASW][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1669870	1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs1669872	1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs16964891	0.95[YRI][hapmap];1.00[AFR][1000 genomes]
rs16964910	0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs16964915	0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs16964919	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs16964921	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs16964928	0.81[ASW][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2242059	0.88[ASN][1000 genomes]
rs2414137	0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2414138	0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2414145	1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs28367336	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28374631	0.98[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28409636	0.98[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28409760	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28475475	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28479614	0.83[AFR][1000 genomes]
rs28496242	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28503750	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28508266	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28532168	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28556657	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28618215	0.81[AFR][1000 genomes]
rs28633243	1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28650960	0.83[AFR][1000 genomes]
rs28653534	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28657676	0.85[AFR][1000 genomes]
rs28693941	0.98[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28756182	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3764230	0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4499185	0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs4624108	0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4774620	1.00[CHD][hapmap]
rs4774621	1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs4776036	0.90[EUR][1000 genomes]
rs4987194	0.83[AFR][1000 genomes]
rs58029714	0.87[AFR][1000 genomes]
rs7163242	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7163778	1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs7164164	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7164872	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7167181	0.83[AFR][1000 genomes]
rs7167680	0.83[AFR][1000 genomes]
rs7168251	0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7169104	0.86[YRI][hapmap]
rs7169346	0.89[MKK][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs7170622	0.87[YRI][hapmap]
rs7171999	0.88[ASN][1000 genomes]
rs73408408	0.83[AFR][1000 genomes]
rs73408415	0.99[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs73408465	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs73408469	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs73408478	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs73410713	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs744501	0.87[MKK][hapmap];0.87[YRI][hapmap]
rs8023623	0.83[AFR][1000 genomes]
rs8024412	0.84[MKK][hapmap]
rs8024624	0.83[AFR][1000 genomes]
rs8027777	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8030307	0.88[ASN][1000 genomes]
rs8035199	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8040369	0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8041819	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8042235	0.83[YRI][hapmap]
rs8042245	0.83[YRI][hapmap]
rs876549	1.00[CHD][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9744852	0.87[ASW][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9920739	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8040558	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs8040558	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52595400-52614200	Weak transcription	Fetal Lung	lung
2	chr15:52595800-52628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:52596200-52623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:52597800-52629600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr15:52600600-52624200	Weak transcription	Liver	Liver
7	chr15:52600800-52622800	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr15:52601000-52622600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr15:52601200-52615200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:52601200-52622600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:52601600-52622400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:52601600-52622800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:52601800-52616600	Strong transcription	Primary B cells from cord blood	blood
16	chr15:52601800-52621400	Weak transcription	Psoas Muscle	Psoas
17	chr15:52602000-52622800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:52602200-52622600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr15:52602600-52622800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr15:52603200-52616400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:52603400-52614800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:52605000-52615000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:52605200-52615000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:52605400-52622800	Strong transcription	HSMMtube	muscle
25	chr15:52606800-52618600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:52607000-52622800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:52607200-52614800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:52607400-52614800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
30	chr15:52608200-52615800	Strong transcription	Adipose Nuclei	Adipose
31	chr15:52608400-52614600	Strong transcription	Fetal Muscle Leg	muscle
32	chr15:52608400-52614800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:52608400-52615600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:52608600-52614800	Strong transcription	Primary T cells from cord blood	blood
35	chr15:52608600-52614800	Strong transcription	Primary hematopoietic stem cells	blood
36	chr15:52608600-52614800	Strong transcription	Fetal Brain Female	brain
37	chr15:52608600-52614800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr15:52608600-52615000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:52608600-52615600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:52608600-52615800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:52608600-52616800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:52608600-52622400	Strong transcription	GM12878-XiMat	blood
43	chr15:52608600-52629200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:52609000-52619600	Weak transcription	HepG2	liver
45	chr15:52609000-52623600	Weak transcription	Hela-S3	cervix
46	chr15:52609600-52614400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr15:52609600-52614800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:52609600-52618600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:52609800-52614200	Strong transcription	Aorta	Aorta
50	chr15:52609800-52614600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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