Variant report

Variant	rs12509589
Chromosome Location	chr4:56050213-56050214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10012700	0.90[EUR][1000 genomes]
rs10014689	0.95[ASN][1000 genomes]
rs10017184	0.98[ASN][1000 genomes]
rs10019018	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030224	0.90[EUR][1000 genomes]
rs10213072	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11133365	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723072	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12152606	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12504287	0.90[EUR][1000 genomes]
rs12716020	0.89[EUR][1000 genomes]
rs12716021	0.89[EUR][1000 genomes]
rs13107781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115127	0.83[EUR][1000 genomes]
rs13128075	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13139198	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13143119	0.83[EUR][1000 genomes]
rs13143543	0.83[EUR][1000 genomes]
rs13146373	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1380072	0.90[EUR][1000 genomes]
rs1380073	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551636	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551637	0.90[EUR][1000 genomes]
rs1551638	0.90[EUR][1000 genomes]
rs17081850	0.90[EUR][1000 genomes]
rs17081852	0.90[EUR][1000 genomes]
rs17081854	0.90[EUR][1000 genomes]
rs17081857	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993584	0.83[EUR][1000 genomes]
rs1993585	0.83[EUR][1000 genomes]
rs1993586	0.83[EUR][1000 genomes]
rs2015048	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085620	0.89[EUR][1000 genomes]
rs2085621	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125486	0.90[EUR][1000 genomes]
rs2125488	0.90[EUR][1000 genomes]
rs28702837	0.93[ASN][1000 genomes]
rs28841975	1.00[ASN][1000 genomes]
rs4241993	0.90[EUR][1000 genomes]
rs4277836	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4458511	0.90[EUR][1000 genomes]
rs4864961	0.90[EUR][1000 genomes]
rs4864963	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6554241	0.90[EUR][1000 genomes]
rs6554242	0.90[EUR][1000 genomes]
rs733378	0.90[EUR][1000 genomes]
rs7696873	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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	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

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56036000-56050600	Weak transcription	Pancreas	Pancrea
2	chr4:56042600-56050600	Weak transcription	Placenta	Placenta
3	chr4:56044200-56050600	Weak transcription	Right Atrium	heart
4	chr4:56044600-56051200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:56046800-56054200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:56047800-56053800	Enhancers	HUVEC	blood vessel
7	chr4:56048000-56050400	Weak transcription	Aorta	Aorta
8	chr4:56048000-56050400	Weak transcription	HSMMtube	muscle
9	chr4:56048000-56050400	Enhancers	NH-A	brain
10	chr4:56048000-56050600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:56048000-56050600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:56048000-56050600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr4:56048000-56050600	Weak transcription	Fetal Lung	lung
14	chr4:56048000-56050600	Weak transcription	Left Ventricle	heart
15	chr4:56048000-56051200	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:56048200-56050400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:56048200-56051000	Weak transcription	Fetal Heart	heart
18	chr4:56048400-56050400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:56048800-56051000	Enhancers	NHDF-Ad	bronchial
20	chr4:56048800-56052000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:56048800-56052400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:56049000-56050600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:56049000-56052400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:56049200-56050400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr4:56049200-56052000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:56049200-56052200	Enhancers	HMEC	breast
27	chr4:56049200-56054200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr4:56049400-56050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:56049400-56051000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:56049600-56050800	Enhancers	NHLF	lung
31	chr4:56049600-56051600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:56049600-56051800	Enhancers	Osteobl	bone
33	chr4:56049600-56052000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:56049800-56051200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:56049800-56051200	Enhancers	HSMM	muscle
36	chr4:56049800-56051400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:56049800-56051600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr4:56049800-56051800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:56049800-56052000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:56050000-56050800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:56050000-56050800	Enhancers	NHEK	skin
42	chr4:56050000-56051000	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr4:56050000-56051800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:56050200-56050400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:56050200-56051000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr4:56050200-56051000	Enhancers	Lung	lung
47	chr4:56050200-56051000	Enhancers	Hela-S3	cervix
48	chr4:56050200-56052800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:56050200-56054000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:56050200-56054200	Enhancers	HUES48 Cell Line	embryonic stem cell

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