Variant report

Variant	rs11139361
Chromosome Location	chr9:72179847-72179848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10123008	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs10780527	0.83[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10780528	0.83[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10780539	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs10867825	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10867828	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs10867830	0.84[CHB][hapmap]
rs11139338	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11139511	0.85[CHB][hapmap]
rs1330334	0.86[CEU][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs1411440	0.92[JPT][hapmap]
rs1556211	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1854702	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1854703	0.87[CEU][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1967880	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1970017	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2026150	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs2309515	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs3927538	0.85[AMR][1000 genomes]
rs4744913	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4744914	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4744917	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4744918	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4744919	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6559643	0.95[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7030393	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7031694	0.86[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs72719029	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7350265	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7850006	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7853783	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7864173	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7871895	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs986352	0.81[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap]
rs987653	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]

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	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1048650	chr9:72028458-72179847	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1039966	chr9:72057304-72181564	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv893437	chr9:72118962-72223176	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1049390	chr9:72168645-72185751	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11139361	GDA	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72163200-72185600	Weak transcription	Aorta	Aorta
2	chr9:72170200-72184200	Weak transcription	Ovary	ovary
3	chr9:72171400-72180000	Weak transcription	Right Atrium	heart
4	chr9:72173800-72188400	Weak transcription	Fetal Lung	lung
5	chr9:72178400-72181400	Enhancers	Fetal Heart	heart
6	chr9:72178600-72180400	Enhancers	Psoas Muscle	Psoas
7	chr9:72178600-72180400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr9:72178600-72181800	Enhancers	Brain Germinal Matrix	brain
9	chr9:72178600-72181800	Enhancers	Fetal Brain Male	brain
10	chr9:72178800-72180000	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:72178800-72180000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr9:72178800-72181400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr9:72179200-72180800	Enhancers	Fetal Brain Female	brain
14	chr9:72179200-72181000	Enhancers	Brain Angular Gyrus	brain
15	chr9:72179200-72181200	Enhancers	Brain Hippocampus Middle	brain
16	chr9:72179400-72180200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr9:72179400-72181000	Enhancers	Brain Substantia Nigra	brain
18	chr9:72179400-72181200	Enhancers	Liver	Liver
19	chr9:72179600-72180000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:72179600-72180200	Enhancers	Brain Cingulate Gyrus	brain
21	chr9:72179600-72180400	Enhancers	Colon Smooth Muscle	Colon
22	chr9:72179600-72180600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr9:72179600-72181000	Enhancers	Left Ventricle	heart
24	chr9:72179800-72180400	Enhancers	Adipose Nuclei	Adipose
25	chr9:72179800-72181000	Enhancers	Right Ventricle	heart
26	chr9:72179800-72181200	Weak transcription	Brain Anterior Caudate	brain
27	chr9:72179800-72184000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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