Variant report

Variant	rs10840419
Chromosome Location	chr11:10486254-10486255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10840420	0.87[ASN][1000 genomes]
rs10840421	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10840422	0.87[ASN][1000 genomes]
rs11042811	0.84[ASN][1000 genomes]
rs11042812	0.84[ASN][1000 genomes]
rs11042830	1.00[CEU][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11604833	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs2071020	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6484290	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7119498	0.81[JPT][hapmap]
rs899010	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs936513	0.86[ASN][1000 genomes]
rs9971562	0.89[CHB][hapmap];0.81[JPT][hapmap]

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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv896990	chr11:10458596-10514707	Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10840419	AMPD3	cis	thalamus	BrainEAC
rs10840419	AMPD3	cis	parietal	SCAN
rs10840419	ARFIP2	cis	parietal	SCAN
rs10840419	OLFML1	cis	cerebellum	SCAN
rs10840419	OR10A6	cis	parietal	SCAN
rs10840419	OR2AG2	cis	parietal	SCAN
rs10840419	AMPD3	cis	brain	BrainEAC

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10473200-10512000	Weak transcription	Aorta	Aorta
2	chr11:10477800-10489000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:10478000-10487400	Weak transcription	HMEC	breast
4	chr11:10478400-10487200	Weak transcription	Fetal Intestine Large	intestine
5	chr11:10478400-10487400	Weak transcription	Right Ventricle	heart
6	chr11:10478400-10489000	Weak transcription	A549	lung
7	chr11:10478400-10500000	Weak transcription	Fetal Intestine Small	intestine
8	chr11:10478400-10502800	Weak transcription	Pancreas	Pancrea
9	chr11:10478800-10493600	Weak transcription	HSMM	muscle
10	chr11:10478800-10511600	Weak transcription	Psoas Muscle	Psoas
11	chr11:10479000-10502800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:10479800-10519400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:10481000-10488000	Weak transcription	Fetal Stomach	stomach
14	chr11:10481200-10486400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:10481200-10487600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:10481200-10494600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:10481400-10486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:10481400-10487200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr11:10481400-10488400	Weak transcription	NHDF-Ad	bronchial
20	chr11:10482400-10489000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr11:10482600-10486600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:10482600-10486800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:10482600-10488000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:10482600-10488400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:10482600-10488600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:10482600-10489000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:10482600-10489200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr11:10482800-10487200	Strong transcription	Dnd41	blood
29	chr11:10482800-10487600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:10482800-10488000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr11:10482800-10488600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr11:10482800-10488600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr11:10482800-10488600	Strong transcription	Thymus	Thymus
34	chr11:10482800-10488800	Strong transcription	Primary T cells from cord blood	blood
35	chr11:10482800-10488800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:10483000-10486400	Strong transcription	Brain Anterior Caudate	brain
37	chr11:10483000-10487200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr11:10483000-10487200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr11:10483000-10487200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:10483000-10487400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:10483000-10487400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr11:10483000-10488800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:10483000-10489000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:10483200-10486600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr11:10483200-10486600	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr11:10483200-10487200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr11:10483200-10487200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:10483200-10488200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:10483200-10489000	Strong transcription	Fetal Thymus	thymus
50	chr11:10483200-10489200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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