Variant report

Variant	rs59228485
Chromosome Location	chr2:54904880-54904881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54903620..54905654-chr2:54949868..54952603,2	K562	blood:
2	chr2:54342492..54344341-chr2:54902621..54905084,2	MCF-7	breast:
3	chr2:54903042..54905906-chr2:54907957..54909608,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214595	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13405115	1.00[ASN][1000 genomes]
rs17343918	1.00[ASN][1000 genomes]
rs17344134	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17344169	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17344176	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17344287	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17344308	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17344343	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415829	1.00[ASN][1000 genomes]
rs17415857	1.00[ASN][1000 genomes]
rs17416130	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17416291	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17416820	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521468	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17521510	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17580255	1.00[ASN][1000 genomes]
rs17580855	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17580876	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1804472	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3796015	0.82[EUR][1000 genomes]
rs41281495	0.91[EUR][1000 genomes]
rs41281497	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258834	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4440005	0.82[EUR][1000 genomes]
rs57810131	1.00[ASN][1000 genomes]
rs58143357	1.00[ASN][1000 genomes]
rs61480394	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755737	0.91[EUR][1000 genomes]
rs72911560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911563	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72915032	1.00[ASN][1000 genomes]
rs72915529	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73932786	1.00[ASN][1000 genomes]
rs73932787	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54897200-54907800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:54898200-54907000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:54898600-54907800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:54900000-54908600	Enhancers	NHDF-Ad	bronchial
5	chr2:54901000-54907000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:54901000-54907800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:54901200-54907800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:54901400-54905000	Weak transcription	Primary B cells from cord blood	blood
9	chr2:54901400-54907600	Weak transcription	HMEC	breast
10	chr2:54901400-54908600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:54901800-54907800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:54902000-54906000	Enhancers	Osteobl	bone
13	chr2:54902000-54907000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:54902000-54907000	Weak transcription	Brain Anterior Caudate	brain
15	chr2:54902200-54907800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr2:54902400-54907000	Weak transcription	Brain Substantia Nigra	brain
17	chr2:54902600-54907600	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:54903000-54907600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:54903400-54905000	Enhancers	HSMMtube	muscle
20	chr2:54903400-54907000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:54903400-54907600	Weak transcription	Liver	Liver
22	chr2:54903400-54907800	Weak transcription	Pancreas	Pancrea
23	chr2:54903400-54908800	Weak transcription	Spleen	Spleen
24	chr2:54903400-54915600	Weak transcription	Right Atrium	heart
25	chr2:54903600-54907000	Weak transcription	Right Ventricle	heart
26	chr2:54904000-54905200	Weak transcription	NH-A	brain
27	chr2:54904000-54907000	Weak transcription	Left Ventricle	heart
28	chr2:54904000-54907000	Weak transcription	Lung	lung
29	chr2:54904200-54907600	Weak transcription	HepG2	liver
30	chr2:54904200-54907800	Weak transcription	Fetal Heart	heart
31	chr2:54904400-54907000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:54904400-54907600	Weak transcription	Fetal Thymus	thymus
33	chr2:54904600-54905200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:54904600-54905200	Flanking Active TSS	GM12878-XiMat	blood
35	chr2:54904600-54906400	Enhancers	Primary B cells from peripheral blood	blood
36	chr2:54904800-54907200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:54904800-54907600	Weak transcription	NHLF	lung
38	chr2:54904800-54907800	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:54904800-54908000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:54904800-54908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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