Variant report

Variant	rs10518687
Chromosome Location	chr15:52687433-52687434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52677998..52679632-chr15:52685576..52688227,3	MCF-7	breast:
2	chr15:52686648..52688420-chr15:52703081..52704876,2	MCF-7	breast:
3	chr15:52668451..52670265-chr15:52685218..52687960,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1001522	0.88[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10083671	0.88[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10083673	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1009157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10467925	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1125460	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12324100	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12324121	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs12898655	0.89[ASN][1000 genomes]
rs12909874	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12914979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1464963	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1464964	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1669856	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1669858	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1669867	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs1724628	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]
rs1724629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1724631	0.95[GIH][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1724634	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1724639	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1724641	0.85[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17542017	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17613475	0.96[MEX][hapmap]
rs2242057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2242058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2414150	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414151	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2444013	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2950056	0.89[GIH][hapmap]
rs35134548	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35523401	0.87[ASN][1000 genomes]
rs3858907	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4280181	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs4519295	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4606660	0.88[EUR][1000 genomes]
rs4776037	0.91[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4776039	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4776046	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62015999	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62023267	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71474804	0.93[ASN][1000 genomes]
rs7176061	0.83[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs7176482	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7176639	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7182150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs722436	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs752865	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs752866	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs8028033	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8033626	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8038386	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs935892	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]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10518687	SPPL2A	cis	parietal	SCAN
rs10518687	MYO5A	cis	cerebellum	SCAN
rs10518687	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs10518687	SHC4	cis	cerebellum	SCAN
rs10518687	MYO5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
2	chr15:52647400-52690600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:52663200-52711400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr15:52663400-52708600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr15:52665200-52720600	Weak transcription	Pancreas	Pancrea
6	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
7	chr15:52669400-52693400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:52674000-52703800	Weak transcription	Fetal Brain Male	brain
10	chr15:52675000-52697400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr15:52676000-52705600	Weak transcription	Fetal Stomach	stomach
12	chr15:52676200-52696800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:52676200-52701800	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:52676400-52696800	Weak transcription	Brain Germinal Matrix	brain
15	chr15:52676400-52696800	Weak transcription	Dnd41	blood
16	chr15:52676400-52697000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:52676400-52699600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr15:52676400-52701000	Weak transcription	HMEC	breast
19	chr15:52676400-52709800	Weak transcription	NHLF	lung
20	chr15:52676400-52721400	Weak transcription	Gastric	stomach
21	chr15:52676600-52689000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr15:52676600-52698000	Weak transcription	Fetal Thymus	thymus
23	chr15:52676600-52701800	Weak transcription	Right Ventricle	heart
24	chr15:52676600-52706400	Weak transcription	Lung	lung
25	chr15:52676600-52718600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:52677000-52730000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr15:52677800-52689200	Weak transcription	Brain Anterior Caudate	brain
28	chr15:52679800-52729600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
30	chr15:52680600-52719800	Weak transcription	NH-A	brain
31	chr15:52680800-52716400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:52680800-52730000	Weak transcription	Brain Angular Gyrus	brain
33	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
34	chr15:52681000-52696600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:52681000-52696800	Weak transcription	Ovary	ovary
36	chr15:52681000-52706800	Weak transcription	Brain Substantia Nigra	brain
37	chr15:52681200-52689200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:52681200-52701000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:52682600-52693200	Strong transcription	Primary B cells from cord blood	blood
40	chr15:52683000-52690400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr15:52683400-52687800	Strong transcription	Primary T cells from cord blood	blood
42	chr15:52683800-52696800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:52684000-52689200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr15:52684000-52693600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:52684000-52719800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:52684400-52689200	Weak transcription	Fetal Brain Female	brain
47	chr15:52684400-52696600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:52684400-52696800	Weak transcription	HSMM	muscle
49	chr15:52684600-52695400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:52684800-52688000	Weak transcription	Adipose Nuclei	Adipose

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