Variant report

Variant	rs2125488
Chromosome Location	chr4:56039942-56039943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10012700	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10016792	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10019018	0.93[EUR][1000 genomes]
rs10030224	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10213072	0.84[EUR][1000 genomes]
rs11133363	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11133364	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11133365	0.90[EUR][1000 genomes]
rs12152606	0.84[EUR][1000 genomes]
rs12504287	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12509589	0.90[EUR][1000 genomes]
rs12645088	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12716020	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12716021	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13107781	0.90[EUR][1000 genomes]
rs13115127	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13139198	0.89[EUR][1000 genomes]
rs13143119	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13143543	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1380072	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1380073	0.84[EUR][1000 genomes]
rs1551636	0.90[EUR][1000 genomes]
rs1551637	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1551638	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17081850	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17081852	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17081854	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17081857	0.84[EUR][1000 genomes]
rs1870376	0.80[EUR][1000 genomes]
rs1870381	0.90[EUR][1000 genomes]
rs1870382	0.90[EUR][1000 genomes]
rs1993583	0.80[EUR][1000 genomes]
rs1993584	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1993585	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1993586	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2015048	0.84[EUR][1000 genomes]
rs2085620	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2085621	0.84[EUR][1000 genomes]
rs2125486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2125487	0.80[EUR][1000 genomes]
rs2899030	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3986296	0.80[EUR][1000 genomes]
rs4241993	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4277836	0.84[EUR][1000 genomes]
rs4304028	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4458511	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4864960	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4864961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6554240	0.80[EUR][1000 genomes]
rs6554241	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6554242	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6810735	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6812621	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6852640	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6853855	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs733378	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7435539	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7440118	0.82[AMR][1000 genomes]
rs7696873	0.84[EUR][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	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3386424	chr4:56039883-56040051	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56035800-56042200	Weak transcription	Right Atrium	heart
2	chr4:56036000-56050600	Weak transcription	Pancreas	Pancrea
3	chr4:56036200-56041800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:56036200-56044400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:56036800-56044600	Weak transcription	Stomach Mucosa	stomach
6	chr4:56037800-56042200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:56038200-56040000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:56038600-56040000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:56038600-56040200	Enhancers	Hela-S3	cervix
10	chr4:56038600-56040200	Enhancers	NH-A	brain
11	chr4:56038600-56040600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr4:56038600-56041600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:56038600-56041600	Enhancers	NHDF-Ad	bronchial
14	chr4:56038800-56040000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:56038800-56040000	Enhancers	HMEC	breast
16	chr4:56038800-56040000	Enhancers	NHEK	skin
17	chr4:56038800-56042000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:56039000-56040200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:56039000-56040200	Enhancers	NHLF	lung
20	chr4:56039000-56040400	Enhancers	Osteobl	bone
21	chr4:56039200-56040200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:56039200-56040800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:56039200-56041800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr4:56039200-56041800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:56039400-56041600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:56039400-56041600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr4:56039400-56041800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:56039400-56042200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:56039400-56043800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:56039600-56040200	Enhancers	HSMM	muscle
31	chr4:56039600-56040800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:56039600-56041400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:56039600-56041600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:56039600-56041600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:56039600-56041600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:56039600-56041600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:56039600-56042000	Enhancers	HUVEC	blood vessel
38	chr4:56039600-56042200	Weak transcription	Placenta	Placenta
39	chr4:56039600-56043800	Weak transcription	Fetal Muscle Leg	muscle
40	chr4:56039800-56040000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:56039800-56041000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr4:56039800-56041600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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