Variant report

Variant	rs55877758
Chromosome Location	chr2:172409030-172409031
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1047023	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047109	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047255	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17222641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288588	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821083	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55638996	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55852614	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55862034	0.83[ASN][1000 genomes]
rs56228832	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56372408	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72884332	0.83[ASN][1000 genomes]
rs72884356	0.83[ASN][1000 genomes]
rs72884400	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72885909	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72885911	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72885915	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72885917	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585974	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs55877758	CYBRD1	cis	Artery Tibial	GTEx
rs55877758	CYBRD1	Cis_1M	lymphoblastoid	RTeQTL
rs55877758	CYBRD1	cis	Adipose Subcutaneous	GTEx
rs55877758	CYBRD1	cis	Whole Blood	GTEx
rs55877758	CYBRD1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172381000-172410400	Weak transcription	Fetal Thymus	thymus
2	chr2:172381200-172410400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:172386400-172419800	Weak transcription	Lung	lung
4	chr2:172387200-172413800	Weak transcription	Spleen	Spleen
5	chr2:172388000-172411400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:172388200-172411000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:172388400-172411800	Weak transcription	Brain Substantia Nigra	brain
8	chr2:172388600-172412400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:172388800-172410400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:172388800-172411000	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:172388800-172413800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:172388800-172413800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:172388800-172414800	Weak transcription	Brain Angular Gyrus	brain
14	chr2:172388800-172414800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:172389000-172411000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:172392400-172412200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:172394000-172411200	Weak transcription	NHLF	lung
18	chr2:172396600-172414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:172397000-172410200	Weak transcription	Placenta	Placenta
20	chr2:172398200-172414000	Weak transcription	Brain Anterior Caudate	brain
21	chr2:172398400-172411200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:172399400-172409400	Weak transcription	NHEK	skin
23	chr2:172399400-172410400	Weak transcription	Right Ventricle	heart
24	chr2:172399400-172411000	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:172399600-172409600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:172400000-172409800	Weak transcription	K562	blood
27	chr2:172400000-172410200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:172400000-172410200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:172400000-172410200	Weak transcription	Ovary	ovary
30	chr2:172400000-172410400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:172400000-172410400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:172400000-172410400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:172400000-172410400	Weak transcription	Left Ventricle	heart
34	chr2:172400000-172410400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:172400000-172410800	Weak transcription	Fetal Lung	lung
36	chr2:172400000-172411000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:172400000-172416400	Weak transcription	Gastric	stomach
38	chr2:172400200-172413800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:172401400-172410400	Weak transcription	Fetal Stomach	stomach
40	chr2:172401400-172411200	Weak transcription	HUVEC	blood vessel
41	chr2:172403400-172411000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:172403800-172411000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:172403800-172411000	Weak transcription	Aorta	Aorta
44	chr2:172404200-172410400	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:172404400-172409200	Weak transcription	GM12878-XiMat	blood
46	chr2:172404600-172409400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:172404800-172410400	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:172406000-172409200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:172406000-172411200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:172406000-172413800	Weak transcription	Esophagus	oesophagus

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