Variant report

Variant	rs1669877
Chromosome Location	chr15:52697815-52697816
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	chr15:52691750..52693545-chr15:52696504..52698685,2	MCF-7	breast:
2	chr15:52696768..52698806-chr15:52701704..52704430,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1405184	0.82[MEX][hapmap]
rs1526169	0.94[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1534200	0.81[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1615235	0.94[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1669864	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1669866	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1693494	0.82[YRI][hapmap]
rs1724585	0.84[EUR][1000 genomes]
rs1724592	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1724595	0.82[YRI][hapmap]
rs1724624	0.87[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1724625	0.89[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1724626	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724627	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724635	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17707852	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1972160	0.94[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2257152	0.82[YRI][hapmap]
rs2290332	0.82[MEX][hapmap]
rs2290335	0.81[CHB][hapmap]
rs2290336	0.82[MEX][hapmap]
rs2444015	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2444019	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2462847	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2462848	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2462849	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2600902	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2693462	0.87[LWK][hapmap]
rs3794565	0.82[MEX][hapmap]
rs3794566	0.82[MEX][hapmap]
rs7175314	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8030535	0.86[MEX][hapmap]
rs8033579	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs871488	0.82[MEX][hapmap]
rs940970	0.82[MEX][hapmap]

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	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
3	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1669877	MYO5A	cis	lymphoblastoid	seeQTL
rs1669877	MYO5A	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
2	chr15:52663200-52711400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:52663400-52708600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:52665200-52720600	Weak transcription	Pancreas	Pancrea
5	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
6	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:52674000-52703800	Weak transcription	Fetal Brain Male	brain
8	chr15:52676000-52705600	Weak transcription	Fetal Stomach	stomach
9	chr15:52676200-52701800	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:52676400-52699600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:52676400-52701000	Weak transcription	HMEC	breast
12	chr15:52676400-52709800	Weak transcription	NHLF	lung
13	chr15:52676400-52721400	Weak transcription	Gastric	stomach
14	chr15:52676600-52698000	Weak transcription	Fetal Thymus	thymus
15	chr15:52676600-52701800	Weak transcription	Right Ventricle	heart
16	chr15:52676600-52706400	Weak transcription	Lung	lung
17	chr15:52676600-52718600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:52677000-52730000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:52679800-52729600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
21	chr15:52680600-52719800	Weak transcription	NH-A	brain
22	chr15:52680800-52716400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:52680800-52730000	Weak transcription	Brain Angular Gyrus	brain
24	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
25	chr15:52681000-52706800	Weak transcription	Brain Substantia Nigra	brain
26	chr15:52681200-52701000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:52684000-52719800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:52684800-52701000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:52684800-52719800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr15:52684800-52730000	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:52685000-52701200	Weak transcription	A549	lung
32	chr15:52685000-52717000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:52685200-52701000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:52685400-52698800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:52685400-52706200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr15:52685400-52711000	Weak transcription	NHDF-Ad	bronchial
37	chr15:52685400-52730000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr15:52685600-52708000	Weak transcription	NHEK	skin
39	chr15:52687000-52698600	Weak transcription	Fetal Muscle Leg	muscle
40	chr15:52687000-52700600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:52687000-52714800	Weak transcription	Psoas Muscle	Psoas
42	chr15:52687000-52715000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:52687200-52706200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr15:52689600-52707400	Weak transcription	Fetal Heart	heart
45	chr15:52689600-52730200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:52689600-52730200	Weak transcription	Left Ventricle	heart
47	chr15:52689600-52730400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:52689800-52703000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:52689800-52706800	Weak transcription	HSMMtube	muscle
50	chr15:52690000-52700600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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