Variant report

Variant	rs10885586
Chromosome Location	chr10:116357563-116357564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10159807	0.82[EUR][1000 genomes]
rs10159811	0.83[EUR][1000 genomes]
rs10159857	0.83[EUR][1000 genomes]
rs10749167	0.83[EUR][1000 genomes]
rs10749168	0.84[EUR][1000 genomes]
rs10787533	0.91[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs10787534	0.82[EUR][1000 genomes]
rs10787535	0.84[EUR][1000 genomes]
rs10787538	0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10885574	0.82[EUR][1000 genomes]
rs10885576	0.83[EUR][1000 genomes]
rs10885578	0.84[EUR][1000 genomes]
rs10885579	0.91[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs10885581	0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10885582	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10885583	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10885585	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11196775	0.90[MEX][hapmap]
rs11196782	0.84[EUR][1000 genomes]
rs11196783	0.84[EUR][1000 genomes]
rs11196784	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11196786	0.89[EUR][1000 genomes]
rs11196790	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196793	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196794	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11196796	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11196797	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12357781	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12772307	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1333686	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1333690	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752016	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7893570	0.83[EUR][1000 genomes]
rs7923449	0.82[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10885586	PNLIPRP2	cis	cerebellum	SCAN
rs10885586	ABLIM1	cis	multi-tissue	Pritchard

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116336800-116359800	Weak transcription	Lung	lung
2	chr10:116336800-116360000	Weak transcription	Fetal Muscle Leg	muscle
3	chr10:116337000-116360200	Weak transcription	Esophagus	oesophagus
4	chr10:116337800-116362600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:116342200-116359800	Weak transcription	Adipose Nuclei	Adipose
6	chr10:116345000-116382400	Weak transcription	HSMM	muscle
7	chr10:116345800-116364000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr10:116346200-116360000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:116350600-116358800	Weak transcription	Liver	Liver
10	chr10:116352200-116360600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr10:116352600-116360000	Weak transcription	Fetal Intestine Large	intestine
12	chr10:116352600-116367600	Weak transcription	Ovary	ovary
13	chr10:116353000-116364200	Weak transcription	Psoas Muscle	Psoas
14	chr10:116353200-116364600	Weak transcription	Brain Hippocampus Middle	brain
15	chr10:116353400-116360000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr10:116353400-116361200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr10:116353400-116364000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr10:116353600-116359200	Weak transcription	Fetal Intestine Small	intestine
19	chr10:116353600-116360000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:116353800-116358600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr10:116354000-116359800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr10:116354200-116360200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:116354200-116360600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr10:116354600-116364600	Weak transcription	Gastric	stomach
25	chr10:116354800-116360000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr10:116354800-116378600	Weak transcription	Fetal Stomach	stomach
27	chr10:116355000-116363000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr10:116355400-116359800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr10:116355400-116364200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr10:116355400-116371000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr10:116355600-116358000	Genic enhancers	Left Ventricle	heart
32	chr10:116356000-116357800	Enhancers	Right Atrium	heart
33	chr10:116356400-116357600	Genic enhancers	Fetal Heart	heart
34	chr10:116356400-116357800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr10:116356400-116364000	Weak transcription	Fetal Kidney	kidney
36	chr10:116356400-116364200	Weak transcription	Brain Substantia Nigra	brain
37	chr10:116356600-116360000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr10:116356600-116364200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr10:116356800-116357800	Enhancers	Brain Anterior Caudate	brain
40	chr10:116356800-116359800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr10:116357000-116363000	Weak transcription	HepG2	liver
42	chr10:116357200-116360200	Weak transcription	HSMMtube	muscle
43	chr10:116357400-116357600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr10:116357400-116357600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr10:116357400-116357600	Genic enhancers	Pancreas	Pancrea
46	chr10:116357400-116357800	Genic enhancers	Right Ventricle	heart
47	chr10:116357400-116358200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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