Variant report

Variant	rs11239559
Chromosome Location	chr10:46057222-46057223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:46049227..46053354-chr10:46053983..46058180,6	K562	blood:
2	chr10:46054558..46056066-chr10:46056809..46059379,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10793618	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10793621	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1080264	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11239558	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239564	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239565	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239567	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239570	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239577	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239585	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11239587	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11528544	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12217545	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12766066	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1565096	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1565097	0.87[EUR][1000 genomes]
rs1982794	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1982795	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1994426	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3740107	0.88[EUR][1000 genomes]
rs3824617	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4948673	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4949003	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7074524	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7095806	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73289207	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7900810	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7900977	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7918454	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1043536	chr10:45915941-46076235	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv895111	chr10:45989745-46071900	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv528750	chr10:46024620-46076235	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	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
11	nsv1047117	chr10:46027942-46075946	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11239559	AGAP4	cis	Artery Tibial	GTEx
rs11239559	AGAP4	cis	Skin Sun Exposed Lower leg	GTEx
rs11239559	ZFAND4	cis	Nerve Tibial	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46014400-46070000	Weak transcription	Psoas Muscle	Psoas
2	chr10:46026200-46057600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:46028800-46069200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr10:46042000-46062600	Weak transcription	Aorta	Aorta
5	chr10:46043400-46057800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr10:46044400-46057800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr10:46045000-46058600	Weak transcription	Fetal Stomach	stomach
8	chr10:46046200-46057400	Weak transcription	Fetal Muscle Leg	muscle
9	chr10:46047000-46076400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:46049400-46065200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr10:46051800-46057600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:46054200-46057400	Weak transcription	Right Ventricle	heart
13	chr10:46054200-46057600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr10:46054200-46057800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr10:46054200-46057800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:46054200-46057800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:46054200-46057800	Weak transcription	Brain Substantia Nigra	brain
18	chr10:46054200-46058000	Weak transcription	Fetal Lung	lung
19	chr10:46054200-46058200	Weak transcription	K562	blood
20	chr10:46054200-46060600	Weak transcription	Left Ventricle	heart
21	chr10:46054200-46075600	Weak transcription	Primary T cells from cord blood	blood
22	chr10:46054200-46075800	Weak transcription	Right Atrium	heart
23	chr10:46054400-46057800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr10:46054400-46057800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr10:46054400-46058200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:46054400-46058400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr10:46054400-46067400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr10:46054400-46073400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr10:46055000-46058400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:46055000-46058600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr10:46055600-46069400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr10:46055600-46073600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr10:46056200-46057400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr10:46056200-46058200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr10:46056200-46058400	Weak transcription	Gastric	stomach
36	chr10:46056200-46058400	Weak transcription	Pancreas	Pancrea
37	chr10:46056200-46061800	Weak transcription	Brain Hippocampus Middle	brain
38	chr10:46056200-46061800	Weak transcription	Ovary	ovary
39	chr10:46056200-46064400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr10:46056200-46069400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr10:46056200-46075000	Weak transcription	Primary B cells from cord blood	blood
42	chr10:46056200-46075200	Weak transcription	Thymus	Thymus
43	chr10:46056400-46057600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr10:46056400-46069400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr10:46056400-46073400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr10:46056600-46057600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:46056600-46061400	Weak transcription	Brain Angular Gyrus	brain
48	chr10:46057000-46060000	Weak transcription	Fetal Intestine Small	intestine

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