Variant report

Variant	rs11239585
Chromosome Location	chr10:46153984-46153985
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10793618	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10793621	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1080264	0.86[EUR][1000 genomes]
rs11239558	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239559	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11239564	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11239565	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11239567	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11239570	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11239577	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11239587	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11528544	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12217545	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12766066	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1982794	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1982795	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1994426	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3824617	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4948673	0.80[EUR][1000 genomes]
rs4949003	0.86[EUR][1000 genomes]
rs7074524	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7095806	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73289207	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7900810	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7918454	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1050880	chr10:46091441-46160597	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv540588	chr10:46091441-46160597	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv895113	chr10:46134013-46167847	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3392795	chr10:46147995-46170942	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1045014	chr10:46148750-46814526	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	esv2754498	chr10:46148750-47136996	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv540591	chr10:46153700-47140487	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv1044906	chr10:46153700-47148281	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv540592	chr10:46153700-47148281	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11239585	AGAP4	cis	Artery Tibial	GTEx
rs11239585	ZFAND4	cis	Nerve Tibial	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46090600-46167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:46108000-46155800	Weak transcription	Brain Angular Gyrus	brain
3	chr10:46108400-46167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:46108600-46155400	Weak transcription	Fetal Intestine Small	intestine
5	chr10:46110800-46156800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr10:46120000-46157800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr10:46122200-46154600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr10:46122200-46157200	Weak transcription	Gastric	stomach
9	chr10:46122400-46156400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr10:46133800-46157800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:46137200-46167000	Weak transcription	Right Ventricle	heart
12	chr10:46137600-46156600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr10:46137600-46167200	Weak transcription	Ovary	ovary
14	chr10:46138400-46156600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr10:46142400-46158000	Weak transcription	A549	lung
16	chr10:46142800-46155200	Weak transcription	Pancreas	Pancrea
17	chr10:46142800-46155600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr10:46142800-46156400	Weak transcription	Fetal Stomach	stomach
19	chr10:46142800-46156800	Weak transcription	Lung	lung
20	chr10:46142800-46167000	Weak transcription	Esophagus	oesophagus
21	chr10:46142800-46167000	Weak transcription	Psoas Muscle	Psoas
22	chr10:46142800-46167000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr10:46142800-46167200	Weak transcription	Aorta	Aorta
24	chr10:46143000-46154400	Weak transcription	Fetal Muscle Leg	muscle
25	chr10:46143000-46156200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr10:46143200-46154400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr10:46143200-46155800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr10:46143200-46167000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr10:46143200-46167200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr10:46143200-46167400	Weak transcription	Left Ventricle	heart
31	chr10:46143400-46155400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr10:46143400-46167000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr10:46143400-46167000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr10:46143600-46154200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:46143600-46167200	Weak transcription	Fetal Lung	lung
36	chr10:46143800-46157400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr10:46144000-46154400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr10:46144000-46155000	Weak transcription	Fetal Intestine Large	intestine
39	chr10:46144000-46156400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr10:46144000-46156600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr10:46144200-46154800	Weak transcription	Fetal Kidney	kidney
42	chr10:46144200-46156200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr10:46144200-46156200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr10:46144200-46156400	Weak transcription	Adipose Nuclei	Adipose
45	chr10:46144400-46156000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr10:46144400-46156200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr10:46147000-46155800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr10:46147200-46155000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr10:46147200-46155600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr10:46147200-46167000	Weak transcription	Duodenum Mucosa	Duodenum

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