Variant report

Variant	rs11490399
Chromosome Location	chr15:55630809-55630810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10851588	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071180	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11071181	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11629613	0.81[ASN][1000 genomes]
rs11632757	0.81[ASN][1000 genomes]
rs11635532	0.87[ASN][1000 genomes]
rs11636687	0.88[ASN][1000 genomes]
rs11638111	0.82[ASN][1000 genomes]
rs11638732	0.80[ASN][1000 genomes]
rs11639453	0.86[ASN][1000 genomes]
rs11855382	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11857303	0.87[ASN][1000 genomes]
rs12050587	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050662	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12050663	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290343	0.94[ASN][1000 genomes]
rs2290344	0.95[ASN][1000 genomes]
rs2305424	0.85[ASN][1000 genomes]
rs2414409	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2444038	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28540063	0.87[ASN][1000 genomes]
rs28636865	0.81[ASN][1000 genomes]
rs28657774	0.96[ASN][1000 genomes]
rs28668016	0.89[ASN][1000 genomes]
rs28680176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706887	0.95[ASN][1000 genomes]
rs28748576	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34848296	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3743203	0.80[ASN][1000 genomes]
rs4774760	0.86[ASN][1000 genomes]
rs4774764	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774766	0.82[ASN][1000 genomes]
rs55661134	0.90[ASN][1000 genomes]
rs55933611	0.90[ASN][1000 genomes]
rs56257633	0.90[ASN][1000 genomes]
rs58701687	0.87[ASN][1000 genomes]
rs60338710	0.80[ASN][1000 genomes]
rs61573749	0.80[ASN][1000 genomes]
rs67230579	0.88[ASN][1000 genomes]
rs67603645	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7162777	0.86[ASN][1000 genomes]
rs7174876	0.95[ASN][1000 genomes]
rs7183157	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7183960	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72742273	0.86[ASN][1000 genomes]
rs72742282	0.82[ASN][1000 genomes]
rs8024695	0.82[ASN][1000 genomes]
rs9920058	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9920522	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers 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 miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv904243	chr15:55627528-55734158	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11490399	PIGB	Cis_1M	lymphoblastoid	RTeQTL
rs11490399	PIGB	cis	Nerve Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55640000	Weak transcription	Gastric	stomach
2	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
3	chr15:55612000-55635400	Weak transcription	Fetal Brain Female	brain
4	chr15:55612000-55636000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:55612000-55636000	Weak transcription	Brain Germinal Matrix	brain
6	chr15:55612000-55636400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:55612000-55665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
9	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
10	chr15:55612400-55631000	Weak transcription	HSMMtube	muscle
11	chr15:55612400-55635600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:55612600-55640400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:55612600-55650200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:55612600-55663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:55612600-55675600	Weak transcription	Aorta	Aorta
16	chr15:55612800-55631400	Weak transcription	NH-A	brain
17	chr15:55612800-55635800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:55612800-55640400	Weak transcription	NHLF	lung
19	chr15:55612800-55649600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:55612800-55677600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:55613600-55631800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:55614800-55649000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:55617000-55635400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:55617000-55635600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:55617400-55631200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:55618800-55633800	Weak transcription	Stomach Mucosa	stomach
27	chr15:55619600-55633600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:55619600-55633800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:55619600-55640000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:55619800-55632200	Strong transcription	Adipose Nuclei	Adipose
31	chr15:55619800-55635400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:55619800-55636000	Weak transcription	HMEC	breast
33	chr15:55619800-55637600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr15:55620400-55658000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:55620800-55636800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:55621000-55635200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr15:55621600-55636800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr15:55621800-55635400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:55623000-55652600	Weak transcription	Psoas Muscle	Psoas
40	chr15:55623400-55642200	Weak transcription	Hela-S3	cervix
41	chr15:55623600-55635600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr15:55623600-55636000	Weak transcription	NHDF-Ad	bronchial
43	chr15:55623800-55635600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:55623800-55660200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr15:55624000-55635800	Weak transcription	NHEK	skin
46	chr15:55624000-55642800	Weak transcription	Esophagus	oesophagus
47	chr15:55624200-55640400	Weak transcription	Spleen	Spleen
48	chr15:55624800-55635400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr15:55625000-55631200	Strong transcription	Fetal Thymus	thymus
50	chr15:55625000-55636600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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