Variant report

Variant	rs10519911
Chromosome Location	chr4:148550590-148550591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10015717	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1005871	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11099668	0.81[ASN][1000 genomes]
rs12507247	0.90[ASN][1000 genomes]
rs12510847	0.82[ASN][1000 genomes]
rs13108782	0.89[ASN][1000 genomes]
rs17675572	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2036498	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036500	0.95[ASN][1000 genomes]
rs2036501	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2357926	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2654937	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2654938	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2654940	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2654941	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2654948	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2654949	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2718447	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2718448	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2718449	0.95[ASN][1000 genomes]
rs2718452	0.89[ASN][1000 genomes]
rs2718453	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2718454	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2718455	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2718457	0.89[ASN][1000 genomes]
rs2718458	0.94[ASN][1000 genomes]
rs2884383	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4835439	0.86[ASN][1000 genomes]
rs4835440	0.86[ASN][1000 genomes]
rs4835441	0.86[ASN][1000 genomes]
rs4835445	0.88[ASN][1000 genomes]
rs57690385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60862021	0.91[ASN][1000 genomes]
rs6535552	0.89[ASN][1000 genomes]
rs6535553	0.88[ASN][1000 genomes]
rs6535554	0.88[ASN][1000 genomes]
rs6535555	0.83[ASN][1000 genomes]
rs6810521	0.83[ASN][1000 genomes]
rs6828566	0.82[ASN][1000 genomes]
rs6841745	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6845224	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6845592	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6846220	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7655893	0.90[ASN][1000 genomes]
rs7660361	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7664244	0.84[ASN][1000 genomes]
rs7666065	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7672671	0.86[ASN][1000 genomes]
rs7675850	0.90[ASN][1000 genomes]
rs7678612	0.83[ASN][1000 genomes]
rs7687368	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7690974	0.87[ASN][1000 genomes]
rs884761	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs905607	0.81[ASN][1000 genomes]
rs924783	0.87[ASN][1000 genomes]
rs9998065	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830110	chr4:148432125-148595119	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv428776	chr4:148432125-148595119	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1019205	chr4:148524852-148576265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10519911	C10orf99	trans	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148539400-148576800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:148539600-148554200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:148539800-148557200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:148540800-148561000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:148541400-148554800	Weak transcription	A549	lung
6	chr4:148541400-148563400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:148542200-148564200	Strong transcription	Fetal Thymus	thymus
8	chr4:148542400-148560400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr4:148542400-148562200	Weak transcription	Fetal Brain Male	brain
10	chr4:148542400-148575000	Weak transcription	Small Intestine	intestine
11	chr4:148542400-148576600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:148542600-148554000	Weak transcription	Brain Anterior Caudate	brain
13	chr4:148542600-148557000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:148542600-148565200	Weak transcription	Fetal Heart	heart
15	chr4:148542600-148567400	Weak transcription	Stomach Mucosa	stomach
16	chr4:148543000-148560400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:148543200-148550800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:148543200-148551200	Strong transcription	Primary T cells from cord blood	blood
19	chr4:148543200-148559600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:148543200-148560800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr4:148543400-148553600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:148543600-148559000	Strong transcription	Placenta	Placenta
23	chr4:148543600-148560000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr4:148543800-148550600	Strong transcription	Fetal Brain Female	brain
25	chr4:148543800-148550800	Strong transcription	Fetal Intestine Large	intestine
26	chr4:148543800-148551600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:148543800-148552400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:148543800-148558200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:148543800-148558800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr4:148543800-148559000	Strong transcription	Osteobl	bone
31	chr4:148543800-148559800	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr4:148543800-148560000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr4:148543800-148560200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:148543800-148560200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:148543800-148560400	Strong transcription	HSMM	muscle
36	chr4:148543800-148563800	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:148543800-148564200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:148543800-148565400	Strong transcription	Liver	Liver
39	chr4:148544000-148554200	Weak transcription	Brain Angular Gyrus	brain
40	chr4:148544000-148558800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr4:148544000-148560000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:148544200-148553000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:148544200-148557000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:148544400-148560200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr4:148544600-148550600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr4:148544600-148553000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:148544600-148560600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:148545000-148550600	Strong transcription	NH-A	brain
49	chr4:148545000-148551000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:148545000-148552400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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