Variant report

Variant	rs55890437
Chromosome Location	chr4:57235759-57235760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1140982	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11940993	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12640212	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12650288	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1579019	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17086759	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086773	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086801	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17086804	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17086830	0.83[EUR][1000 genomes]
rs17086838	0.81[EUR][1000 genomes]
rs2271924	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34398021	0.83[EUR][1000 genomes]
rs35854625	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3733324	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733326	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796539	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796540	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796549	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796550	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4076103	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41498446	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55778537	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55903333	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55909588	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56095772	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56129706	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56296497	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56362514	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56406704	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57233429	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58654038	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59062367	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59153415	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59278715	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59764923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59828502	0.83[EUR][1000 genomes]
rs7437839	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7688482	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
7	esv3348820	chr4:57235737-57235992	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55890437	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
2	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
3	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
5	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
6	chr4:57203200-57251800	Weak transcription	A549	lung
7	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:57204000-57252200	Weak transcription	NH-A	brain
9	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
11	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:57211000-57251600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr4:57211800-57252200	Weak transcription	Fetal Heart	heart
14	chr4:57212400-57251800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr4:57213000-57244200	Weak transcription	Spleen	Spleen
16	chr4:57213400-57251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:57213400-57252200	Weak transcription	NHLF	lung
18	chr4:57213600-57250200	Weak transcription	K562	blood
19	chr4:57213600-57252000	Weak transcription	HMEC	breast
20	chr4:57214400-57251800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:57214600-57252200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:57215000-57238000	Weak transcription	Brain Substantia Nigra	brain
23	chr4:57215800-57251600	Weak transcription	Brain Anterior Caudate	brain
24	chr4:57216000-57235800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:57216000-57236400	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:57216000-57241200	Weak transcription	Pancreas	Pancrea
27	chr4:57216000-57251800	Weak transcription	HepG2	liver
28	chr4:57216000-57252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:57216000-57253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:57216200-57245600	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:57216200-57246000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:57216200-57246200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:57216400-57251800	Weak transcription	Psoas Muscle	Psoas
34	chr4:57218400-57239000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr4:57218400-57241200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:57219400-57235800	Weak transcription	Left Ventricle	heart
37	chr4:57219400-57236000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:57219800-57236400	Weak transcription	Primary T cells from cord blood	blood
39	chr4:57220400-57236000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr4:57220600-57243400	Weak transcription	HSMM	muscle
41	chr4:57221800-57236000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:57222800-57235800	Weak transcription	Fetal Brain Female	brain
43	chr4:57223000-57235800	Weak transcription	Aorta	Aorta
44	chr4:57223000-57236200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:57223000-57238000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:57223000-57253200	Weak transcription	Esophagus	oesophagus
47	chr4:57223200-57236000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr4:57223200-57253200	Weak transcription	Gastric	stomach
49	chr4:57223600-57251600	Weak transcription	Fetal Kidney	kidney
50	chr4:57225000-57243600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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