Variant report

Variant	rs11239569
Chromosome Location	chr10:46086350-46086351
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10466245	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900221	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900223	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900224	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900229	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900230	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900232	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239528	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239536	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239538	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239545	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239549	0.94[EUR][1000 genomes]
rs11239551	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239571	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242611	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12243153	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246131	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249012	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257537	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12257549	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12269403	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2291428	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291429	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3802548	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55665473	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58865519	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59390133	0.93[ASN][1000 genomes]
rs61854096	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854123	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854156	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7076198	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086046	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72796498	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970548	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1041417	chr10:46021181-46088061	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1052233	chr10:46024620-46088061	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2761592	chr10:46072872-46090202	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11239569	ALOX5	Cis_1M	lymphoblastoid	RTeQTL
rs11239569	FAM21A///FAM21B	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46072600-46086600	Weak transcription	Small Intestine	intestine
2	chr10:46076800-46087000	Weak transcription	Brain Hippocampus Middle	brain
3	chr10:46076800-46087800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr10:46076800-46087800	Weak transcription	Brain Angular Gyrus	brain
5	chr10:46076800-46088000	Weak transcription	Colonic Mucosa	Colon
6	chr10:46076800-46088000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr10:46076800-46089000	Weak transcription	Right Ventricle	heart
8	chr10:46077400-46087800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr10:46077400-46087800	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:46077600-46087400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:46077600-46088400	Weak transcription	Osteobl	bone
12	chr10:46077800-46087000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr10:46077800-46087400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr10:46077800-46087800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr10:46077800-46088400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr10:46077800-46088400	Weak transcription	NHLF	lung
17	chr10:46078000-46087200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr10:46078200-46087000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr10:46078200-46088000	Weak transcription	Fetal Intestine Large	intestine
20	chr10:46080200-46088000	Weak transcription	Hela-S3	cervix
21	chr10:46080400-46088800	Weak transcription	A549	lung
22	chr10:46081600-46089000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr10:46082000-46087000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:46082400-46088200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr10:46082600-46086800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr10:46082800-46088400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr10:46083400-46086400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr10:46083400-46088800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr10:46083400-46088800	Weak transcription	Aorta	Aorta
30	chr10:46084000-46088400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr10:46084000-46088800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr10:46084000-46088800	Weak transcription	Fetal Intestine Small	intestine
33	chr10:46084400-46088400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr10:46084400-46088800	Weak transcription	Fetal Stomach	stomach
35	chr10:46084600-46087000	Strong transcription	Primary B cells from cord blood	blood
36	chr10:46084600-46087000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr10:46084800-46088000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr10:46084800-46088400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr10:46084800-46088600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr10:46085000-46087200	Weak transcription	HepG2	liver
41	chr10:46085200-46086400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr10:46085400-46088000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr10:46085400-46089400	Weak transcription	Placenta	Placenta
44	chr10:46085600-46088000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr10:46085600-46088000	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr10:46085800-46087000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr10:46085800-46087800	Weak transcription	Adipose Nuclei	Adipose
48	chr10:46085800-46088000	Weak transcription	Brain Anterior Caudate	brain
49	chr10:46085800-46088400	Weak transcription	Fetal Brain Female	brain
50	chr10:46085800-46088800	Weak transcription	Fetal Kidney	kidney

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