Variant report

Variant	rs10885579
Chromosome Location	chr10:116304958-116304959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10159807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10159811	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159857	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749167	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749168	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10787533	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10787534	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10787535	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10787538	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]
rs10885574	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885576	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885581	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885582	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10885583	0.81[CEU][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10885585	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10885586	0.91[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs11196782	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11196783	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196784	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196786	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11196790	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11196793	0.93[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs11196794	0.82[EUR][1000 genomes]
rs11196796	0.91[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs11196797	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12357781	0.81[CEU][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12772307	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1333686	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1333690	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2483535	0.89[YRI][hapmap]
rs2483539	0.89[YRI][hapmap]
rs2483541	0.89[YRI][hapmap]
rs2483543	0.88[YRI][hapmap]
rs2483544	0.89[YRI][hapmap]
rs2483548	0.89[YRI][hapmap]
rs2483552	0.84[YRI][hapmap]
rs2483553	0.89[YRI][hapmap]
rs2497725	0.89[YRI][hapmap]
rs2497730	0.89[YRI][hapmap]
rs2497731	0.89[YRI][hapmap]
rs2497735	0.88[YRI][hapmap]
rs4751583	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7893570	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923449	0.91[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10885579	C10orf84	cis	cerebellum	SCAN
rs10885579	RAB11FIP2	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116287200-116307200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:116287400-116310600	Weak transcription	Brain Angular Gyrus	brain
3	chr10:116287400-116310600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr10:116297600-116305200	Enhancers	Dnd41	blood
5	chr10:116297600-116308600	Enhancers	Primary B cells from peripheral blood	blood
6	chr10:116297800-116308600	Enhancers	Stomach Mucosa	stomach
7	chr10:116298000-116308800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:116298200-116307800	Strong transcription	Fetal Intestine Small	intestine
9	chr10:116298400-116307200	Strong transcription	Liver	Liver
10	chr10:116298400-116307600	Weak transcription	Brain Substantia Nigra	brain
11	chr10:116298400-116310200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr10:116298600-116311600	Weak transcription	Gastric	stomach
13	chr10:116298800-116310400	Weak transcription	Small Intestine	intestine
14	chr10:116298800-116310600	Weak transcription	Colonic Mucosa	Colon
15	chr10:116299600-116308200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:116299800-116308800	Genic enhancers	Left Ventricle	heart
17	chr10:116300000-116306400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr10:116300200-116307400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr10:116300400-116307600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr10:116300600-116310600	Weak transcription	Brain Hippocampus Middle	brain
21	chr10:116300800-116305000	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr10:116301800-116307400	Weak transcription	Placenta	Placenta
23	chr10:116301800-116310600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr10:116301800-116310600	Weak transcription	Fetal Lung	lung
25	chr10:116301800-116310800	Weak transcription	HSMM	muscle
26	chr10:116302400-116305000	Strong transcription	HSMMtube	muscle
27	chr10:116302600-116305000	Enhancers	Duodenum Mucosa	Duodenum
28	chr10:116302800-116307200	Weak transcription	Right Atrium	heart
29	chr10:116303000-116305200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr10:116303200-116305000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr10:116303200-116305200	Enhancers	NHEK	skin
32	chr10:116303200-116305400	Enhancers	HMEC	breast
33	chr10:116303200-116306800	Weak transcription	HUVEC	blood vessel
34	chr10:116303400-116305200	Strong transcription	Lung	lung
35	chr10:116303400-116305600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr10:116303400-116306000	Enhancers	Primary hematopoietic stem cells	blood
37	chr10:116303400-116306000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr10:116303600-116305200	Strong transcription	Fetal Intestine Large	intestine
39	chr10:116303600-116305200	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr10:116303600-116305600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr10:116303800-116305200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr10:116303800-116307600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr10:116304000-116305000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr10:116304000-116305200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:116304000-116305200	Enhancers	Esophagus	oesophagus
46	chr10:116304000-116306600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr10:116304000-116307200	Enhancers	Primary B cells from cord blood	blood
48	chr10:116304000-116307800	Strong transcription	Right Ventricle	heart
49	chr10:116304000-116310600	Weak transcription	Brain Anterior Caudate	brain
50	chr10:116304000-116310600	Weak transcription	Brain Cingulate Gyrus	brain

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