Variant report

Variant	rs10787538
Chromosome Location	chr10:116315951-116315952
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10159807	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10159811	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10159857	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10749167	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10749168	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10787533	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10787534	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10787535	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885574	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885576	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885578	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885579	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885581	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885582	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10885583	0.88[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10885585	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10885586	0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11196775	0.90[MEX][hapmap]
rs11196782	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11196783	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11196784	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11196786	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196790	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11196793	0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11196794	0.85[EUR][1000 genomes]
rs11196796	0.84[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11196797	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12357781	0.88[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12772307	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1333686	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1333688	0.86[AFR][1000 genomes]
rs1333690	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2483534	0.84[AFR][1000 genomes]
rs2483535	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2483536	0.83[AFR][1000 genomes]
rs2483537	0.84[AFR][1000 genomes]
rs2483539	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2483540	0.86[AFR][1000 genomes]
rs2483541	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2483542	0.86[AFR][1000 genomes]
rs2483543	0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs2483544	0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs2483545	0.86[AFR][1000 genomes]
rs2483546	0.86[AFR][1000 genomes]
rs2483548	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2483550	0.84[AFR][1000 genomes]
rs2483552	0.81[LWK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs2483553	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2483554	0.86[AFR][1000 genomes]
rs2483555	0.86[AFR][1000 genomes]
rs2483556	0.86[AFR][1000 genomes]
rs2497725	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2497727	0.84[AFR][1000 genomes]
rs2497728	0.86[AFR][1000 genomes]
rs2497729	0.86[AFR][1000 genomes]
rs2497730	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2497731	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2497732	0.86[AFR][1000 genomes]
rs2497735	0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs2497736	0.86[AFR][1000 genomes]
rs2497737	0.86[AFR][1000 genomes]
rs2497738	0.86[AFR][1000 genomes]
rs2497739	0.86[AFR][1000 genomes]
rs4752016	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56757634	0.82[AFR][1000 genomes]
rs58567137	0.84[AFR][1000 genomes]
rs7091986	0.86[AFR][1000 genomes]
rs7893570	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7915116	0.86[AFR][1000 genomes]
rs7915452	0.86[AFR][1000 genomes]
rs7923449	0.91[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10787538	C10orf84	cis	cerebellum	SCAN
rs10787538	NRAP	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116305000-116317600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr10:116305200-116316000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:116305200-116318200	Weak transcription	Fetal Intestine Large	intestine
4	chr10:116307600-116316000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:116307800-116317600	Weak transcription	Fetal Intestine Small	intestine
6	chr10:116309000-116316400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:116310800-116317400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:116311000-116317400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr10:116311000-116331400	Weak transcription	Fetal Brain Male	brain
10	chr10:116311600-116336600	Weak transcription	Colonic Mucosa	Colon
11	chr10:116311800-116317800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr10:116312000-116316800	Weak transcription	Lung	lung
13	chr10:116312000-116317200	Enhancers	Fetal Heart	heart
14	chr10:116312000-116324800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr10:116312000-116331000	Weak transcription	Ovary	ovary
16	chr10:116312000-116334600	Weak transcription	Esophagus	oesophagus
17	chr10:116312000-116335000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr10:116312000-116335200	Weak transcription	Pancreas	Pancrea
19	chr10:116312200-116317600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr10:116312200-116330800	Weak transcription	Adipose Nuclei	Adipose
21	chr10:116312400-116316000	Weak transcription	Psoas Muscle	Psoas
22	chr10:116312400-116316800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:116312400-116316800	Weak transcription	HSMM	muscle
24	chr10:116312400-116331200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr10:116312600-116316000	Weak transcription	Liver	Liver
26	chr10:116312800-116317400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr10:116313000-116317600	Weak transcription	Fetal Muscle Leg	muscle
28	chr10:116313000-116319200	Genic enhancers	Left Ventricle	heart
29	chr10:116313400-116316000	Weak transcription	HSMMtube	muscle
30	chr10:116314000-116316000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:116314200-116316800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr10:116314400-116316000	Weak transcription	Right Atrium	heart
33	chr10:116314600-116317000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr10:116314800-116322400	Weak transcription	Right Ventricle	heart
35	chr10:116315800-116317000	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr10:116315800-116317000	Enhancers	HepG2	liver

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