Variant report

Variant	rs17708103
Chromosome Location	chr15:52803078-52803079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52799417..52803271-chr15:52809477..52812870,3	MCF-7	breast:
2	chr15:52795013..52797872-chr15:52802159..52803968,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231169	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10518684	0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap]
rs10518689	0.93[CHB][hapmap]
rs10518691	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs10518692	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1058219	0.87[CHB][hapmap]
rs11070898	0.86[ASN][1000 genomes]
rs11070900	0.86[ASN][1000 genomes]
rs11852556	0.86[ASN][1000 genomes]
rs11853114	0.93[CHB][hapmap]
rs11853179	0.87[CHB][hapmap]
rs11853237	0.82[ASN][1000 genomes]
rs11853337	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs11853544	0.83[ASN][1000 genomes]
rs11853586	0.93[CHB][hapmap]
rs11854130	0.93[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11854247	0.93[CHB][hapmap]
rs11854456	0.81[ASN][1000 genomes]
rs11854673	0.93[CHB][hapmap]
rs11854780	1.00[CHB][hapmap]
rs11855082	0.93[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11855257	0.87[CHB][hapmap]
rs11855438	0.87[ASN][1000 genomes]
rs11855453	0.93[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11855467	0.80[ASN][1000 genomes]
rs11855584	1.00[CHB][hapmap]
rs11855820	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11855884	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs11856588	0.93[CHB][hapmap]
rs11856662	0.93[CHB][hapmap]
rs11856752	0.93[CHB][hapmap]
rs11856810	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs11856896	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11857854	0.82[ASN][1000 genomes]
rs11857914	0.86[ASN][1000 genomes]
rs11857993	0.93[CHB][hapmap]
rs11858031	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1464965	0.93[CHB][hapmap]
rs1464966	0.93[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1474437	0.93[CHB][hapmap]
rs1474438	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1693492	0.93[CHB][hapmap]
rs1693494	0.93[CHB][hapmap]
rs1693497	0.92[CHB][hapmap]
rs1693501	0.93[CHB][hapmap]
rs1693502	0.93[CHB][hapmap]
rs1693506	0.87[CHB][hapmap]
rs1693507	0.93[CHB][hapmap]
rs1724595	0.93[CHB][hapmap]
rs1724601	0.87[CHB][hapmap]
rs1724603	0.93[CHB][hapmap]
rs1724608	0.91[CHB][hapmap]
rs1724638	0.93[CHB][hapmap]
rs17613951	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17651326	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs17651611	0.93[CHB][hapmap]
rs17651631	0.87[CHB][hapmap]
rs17651692	0.82[ASN][1000 genomes]
rs17651731	1.00[MEX][hapmap]
rs17707941	0.86[ASN][1000 genomes]
rs17707996	1.00[CHB][hapmap]
rs1869126	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1869127	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs1869128	0.93[CHB][hapmap]
rs2140962	0.93[CHB][hapmap]
rs2177876	0.93[CHB][hapmap]
rs2257152	0.93[CHB][hapmap]
rs2272283	0.93[CHB][hapmap]
rs2290334	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2414148	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs2414152	0.84[CHB][hapmap]
rs2693462	0.93[CHB][hapmap]
rs2899488	0.93[CHB][hapmap]
rs34113113	0.86[ASN][1000 genomes]
rs3764227	0.82[ASN][1000 genomes]
rs3816449	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs41408650	0.93[CHB][hapmap]
rs4341694	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4547284	0.84[ASN][1000 genomes]
rs4774624	0.93[CHB][hapmap]
rs4774625	0.92[CHB][hapmap]
rs4774626	0.86[ASN][1000 genomes]
rs4774627	0.93[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4776045	0.93[CHB][hapmap]
rs4776049	0.86[ASN][1000 genomes]
rs4776051	0.93[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs4776053	1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap]
rs56017964	0.87[ASN][1000 genomes]
rs56043792	0.86[ASN][1000 genomes]
rs56312354	1.00[AFR][1000 genomes]
rs56332522	0.83[ASN][1000 genomes]
rs56849428	0.82[ASN][1000 genomes]
rs57364199	0.83[ASN][1000 genomes]
rs58388195	0.83[ASN][1000 genomes]
rs58922508	0.83[ASN][1000 genomes]
rs59477983	0.82[ASN][1000 genomes]
rs61494501	0.84[ASN][1000 genomes]
rs66526357	0.86[ASN][1000 genomes]
rs66674706	0.83[ASN][1000 genomes]
rs67028104	0.86[ASN][1000 genomes]
rs67249415	0.83[ASN][1000 genomes]
rs67287941	0.86[ASN][1000 genomes]
rs67827251	0.86[ASN][1000 genomes]
rs67992061	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs72623985	0.86[ASN][1000 genomes]
rs72623988	0.85[ASN][1000 genomes]
rs72738514	0.83[ASN][1000 genomes]
rs940966	0.93[CHB][hapmap]
rs940971	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs940972	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs940973	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs9788691	0.93[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9788777	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17708103	MYO5A	cis	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52778600-52812400	Weak transcription	Right Ventricle	heart
2	chr15:52786400-52812400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:52789600-52806600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:52792000-52815200	Weak transcription	NHLF	lung
5	chr15:52794600-52803400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:52796800-52803200	Weak transcription	NHDF-Ad	bronchial
7	chr15:52796800-52811200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:52796800-52819400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:52796800-52820000	Weak transcription	Primary T cells from cord blood	blood
10	chr15:52797000-52815200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:52797400-52810200	Weak transcription	Primary B cells from cord blood	blood
12	chr15:52797600-52803200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr15:52797600-52819800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr15:52797800-52803200	Weak transcription	Adipose Nuclei	Adipose
15	chr15:52797800-52805800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:52798200-52803200	Weak transcription	NHEK	skin
17	chr15:52798200-52805800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:52798800-52803800	Enhancers	Brain Cingulate Gyrus	brain
19	chr15:52799400-52804600	Enhancers	Brain Angular Gyrus	brain
20	chr15:52800200-52804000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr15:52800600-52803800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr15:52800600-52804000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:52800800-52803800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:52800800-52808600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:52801000-52808400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:52801200-52804000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:52801400-52803800	Enhancers	Brain Germinal Matrix	brain
28	chr15:52801400-52804000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr15:52801600-52803600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:52801600-52803600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr15:52801600-52803800	Enhancers	Fetal Brain Female	brain
32	chr15:52801600-52804000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:52801800-52810600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:52802000-52803200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:52802000-52809600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:52802200-52803400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr15:52802400-52803400	Enhancers	Right Atrium	heart
38	chr15:52802400-52804000	Enhancers	Brain Hippocampus Middle	brain
39	chr15:52802400-52805200	Enhancers	Brain Anterior Caudate	brain
40	chr15:52802400-52808400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:52802400-52810800	Weak transcription	HSMMtube	muscle
42	chr15:52802600-52803400	Enhancers	Left Ventricle	heart
43	chr15:52802600-52803400	Enhancers	Spleen	Spleen
44	chr15:52802600-52804000	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr15:52802800-52803800	Enhancers	Colon Smooth Muscle	Colon
46	chr15:52802800-52805600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:52802800-52809400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:52803000-52803600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:52803000-52803800	Enhancers	Brain Substantia Nigra	brain
50	chr15:52803000-52803800	Enhancers	Fetal Heart	heart

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