Variant report

Variant	rs935892
Chromosome Location	chr15:52697002-52697003
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	chr15:52691750..52693545-chr15:52696504..52698685,2	MCF-7	breast:
2	chr15:52696768..52698806-chr15:52701704..52704430,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1001522	0.92[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10083671	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10083673	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1009157	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10467925	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10518687	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1125460	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324100	0.88[CEU][hapmap]
rs12324121	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs12898655	0.91[ASN][1000 genomes]
rs12909874	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12914979	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1464963	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1464964	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1669856	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1669858	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1669867	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1724589	0.86[AFR][1000 genomes]
rs1724591	0.89[AFR][1000 genomes]
rs1724628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724629	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724631	0.92[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1724634	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1724639	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1724641	0.96[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17542017	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242057	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2242058	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2414150	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2414151	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs2444013	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950056	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs35134548	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35523401	0.89[ASN][1000 genomes]
rs3858907	0.96[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280181	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4519295	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4776039	0.88[ASN][1000 genomes]
rs4776046	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62023267	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71474804	0.95[ASN][1000 genomes]
rs7176061	0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7176482	0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap]
rs7176639	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs7182150	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs722436	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs752864	0.81[CHB][hapmap]
rs752865	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs752866	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs8028033	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs8033626	0.88[ASN][1000 genomes]
rs8038386	0.84[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	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
rs935892	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs935892	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 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	chr15:52675000-52697400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr15:52676000-52705600	Weak transcription	Fetal Stomach	stomach
10	chr15:52676200-52701800	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:52676400-52699600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:52676400-52701000	Weak transcription	HMEC	breast
13	chr15:52676400-52709800	Weak transcription	NHLF	lung
14	chr15:52676400-52721400	Weak transcription	Gastric	stomach
15	chr15:52676600-52698000	Weak transcription	Fetal Thymus	thymus
16	chr15:52676600-52701800	Weak transcription	Right Ventricle	heart
17	chr15:52676600-52706400	Weak transcription	Lung	lung
18	chr15:52676600-52718600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:52677000-52730000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr15:52679800-52729600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
22	chr15:52680600-52719800	Weak transcription	NH-A	brain
23	chr15:52680800-52716400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:52680800-52730000	Weak transcription	Brain Angular Gyrus	brain
25	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
26	chr15:52681000-52706800	Weak transcription	Brain Substantia Nigra	brain
27	chr15:52681200-52701000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:52684000-52719800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr15:52684800-52701000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr15:52684800-52719800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr15:52684800-52730000	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:52685000-52701200	Weak transcription	A549	lung
33	chr15:52685000-52717000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:52685200-52701000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:52685400-52698800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:52685400-52706200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr15:52685400-52711000	Weak transcription	NHDF-Ad	bronchial
38	chr15:52685400-52730000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:52685600-52708000	Weak transcription	NHEK	skin
40	chr15:52687000-52698600	Weak transcription	Fetal Muscle Leg	muscle
41	chr15:52687000-52700600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:52687000-52714800	Weak transcription	Psoas Muscle	Psoas
43	chr15:52687000-52715000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:52687200-52706200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:52689600-52707400	Weak transcription	Fetal Heart	heart
46	chr15:52689600-52730200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr15:52689600-52730200	Weak transcription	Left Ventricle	heart
48	chr15:52689600-52730400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:52689800-52703000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:52689800-52706800	Weak transcription	HSMMtube	muscle

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