Variant report

Variant	rs10992380
Chromosome Location	chr9:95354524-95354525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10491806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10761156	1.00[YRI][hapmap]
rs10820998	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[CHB][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10821001	0.88[AMR][1000 genomes]
rs10821003	0.88[AMR][1000 genomes]
rs10821004	0.88[AMR][1000 genomes]
rs10821005	0.88[AMR][1000 genomes]
rs10821011	0.87[AMR][1000 genomes]
rs10821014	0.88[AMR][1000 genomes]
rs10992367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992382	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs10992384	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10992390	0.91[CEU][hapmap];0.88[CHB][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992392	0.91[CEU][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992396	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10992406	0.88[CHB][hapmap]
rs10992407	0.82[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10992408	0.88[CHB][hapmap];0.85[AMR][1000 genomes]
rs10992409	0.85[AMR][1000 genomes]
rs10992412	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10992414	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs10992416	0.88[AMR][1000 genomes]
rs10992417	0.88[AMR][1000 genomes]
rs10992420	0.88[AMR][1000 genomes]
rs10992422	0.88[AMR][1000 genomes]
rs10992423	0.88[AMR][1000 genomes]
rs10992437	0.88[AMR][1000 genomes]
rs10992447	0.89[TSI][hapmap]
rs10992448	0.82[CHB][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs10992453	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs10992460	0.82[ASW][hapmap];0.82[CHB][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs10992461	0.82[CHB][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs1117670	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs11533010	0.88[AMR][1000 genomes]
rs12236013	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12236754	0.81[CHB][hapmap];0.84[AMR][1000 genomes]
rs12238691	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs12684587	0.81[AMR][1000 genomes]
rs12685358	0.88[AMR][1000 genomes]
rs12686771	0.89[TSI][hapmap]
rs12686780	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12686781	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1323523	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1326775	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1575460	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17366488	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1853468	0.91[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2025389	1.00[YRI][hapmap]
rs2031262	1.00[YRI][hapmap]
rs2038685	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088054	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088055	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2131919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2146848	0.91[CEU][hapmap]
rs2148537	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2172716	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2181584	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs230222	1.00[YRI][hapmap]
rs331380	1.00[YRI][hapmap]
rs3739605	0.82[CHB][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes]
rs58952648	0.88[AMR][1000 genomes]
rs60498616	0.88[AMR][1000 genomes]
rs6479426	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs67601697	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7031163	0.88[CHB][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs753804	0.88[AMR][1000 genomes]
rs754600	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7853617	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7856147	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7857105	0.91[CEU][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7857502	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7863882	0.83[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs7869603	0.88[AMR][1000 genomes]
rs7875050	0.89[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs912261	0.88[CHB][hapmap];0.87[MEX][hapmap]
rs912264	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs971984	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[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	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1052846	chr9:95291909-95366109	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10992380	ASPN	cis	cerebellum	SCAN
rs10992380	ANKRD19	cis	cerebellum	SCAN
rs10992380	FBP1	cis	cerebellum	SCAN
rs10992380	IARS	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95347600-95365800	Weak transcription	Thymus	Thymus
2	chr9:95347800-95364000	Weak transcription	Left Ventricle	heart
3	chr9:95348800-95355200	Weak transcription	Aorta	Aorta
4	chr9:95351800-95356600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:95352800-95355000	Weak transcription	Fetal Stomach	stomach
6	chr9:95352800-95356200	Weak transcription	Brain Hippocampus Middle	brain
7	chr9:95353000-95355000	Weak transcription	HSMMtube	muscle
8	chr9:95353000-95355200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:95353000-95355200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:95353000-95355400	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:95353000-95362000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:95353200-95355000	Weak transcription	Osteobl	bone
13	chr9:95353200-95355400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:95353200-95355400	Weak transcription	NHDF-Ad	bronchial
15	chr9:95353200-95359400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:95353200-95360600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:95353400-95355000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:95353400-95355200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:95353400-95355400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:95353400-95355400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:95353400-95355400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:95353400-95355400	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:95353600-95355600	Weak transcription	Adipose Nuclei	Adipose
24	chr9:95353800-95355200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:95354000-95355000	Weak transcription	Fetal Lung	lung
26	chr9:95354000-95358400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr9:95354000-95358600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr9:95354000-95362200	Weak transcription	Rectal Smooth Muscle	rectum

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