Variant report

Variant	rs6554241
Chromosome Location	chr4:56042754-56042755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10012700	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10016792	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10019018	0.93[EUR][1000 genomes]
rs10030224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10213072	0.84[EUR][1000 genomes]
rs11133363	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11133364	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11133365	0.90[EUR][1000 genomes]
rs12152606	0.84[EUR][1000 genomes]
rs12504287	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12509589	0.90[EUR][1000 genomes]
rs12645088	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12716020	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12716021	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13107781	0.90[EUR][1000 genomes]
rs13115127	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13139198	0.89[EUR][1000 genomes]
rs13143119	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13143543	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1380072	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1380073	0.84[EUR][1000 genomes]
rs1551636	0.90[EUR][1000 genomes]
rs1551637	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1551638	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17081850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17081852	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17081854	0.80[AFR][1000 genomes];0.95[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	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1993585	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1993586	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2015048	0.84[EUR][1000 genomes]
rs2085620	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2085621	0.84[EUR][1000 genomes]
rs2125486	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2125487	0.80[EUR][1000 genomes]
rs2125488	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2899030	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3986296	0.80[EUR][1000 genomes]
rs4241993	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4277836	0.84[EUR][1000 genomes]
rs4304028	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4458511	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4864960	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4864961	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6554240	0.80[EUR][1000 genomes]
rs6554242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6810735	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6812621	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6852640	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6853855	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs733378	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7435539	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7696873	0.84[EUR][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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56036000-56050600	Weak transcription	Pancreas	Pancrea
2	chr4:56036200-56044400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:56036800-56044600	Weak transcription	Stomach Mucosa	stomach
4	chr4:56039400-56043800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:56039600-56043800	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:56041200-56042800	Enhancers	HSMMtube	muscle
7	chr4:56041400-56042800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:56041400-56042800	Enhancers	HMEC	breast
9	chr4:56041400-56044400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:56041600-56042800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:56041600-56042800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:56041600-56042800	Enhancers	Hela-S3	cervix
13	chr4:56041600-56043000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:56041600-56043000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr4:56041600-56043000	Flanking Active TSS	NH-A	brain
16	chr4:56041800-56042800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:56041800-56042800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:56042000-56042800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr4:56042000-56043000	Enhancers	NHDF-Ad	bronchial
20	chr4:56042000-56043800	Flanking Active TSS	HUVEC	blood vessel
21	chr4:56042200-56042800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr4:56042200-56042800	Enhancers	Left Ventricle	heart
23	chr4:56042200-56042800	Enhancers	Lung	lung
24	chr4:56042200-56043000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr4:56042200-56043000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:56042200-56043000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr4:56042200-56047400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:56042400-56042800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
29	chr4:56042400-56042800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr4:56042400-56044000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:56042400-56047200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:56042400-56047400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:56042400-56047400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:56042400-56047600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:56042400-56049800	Weak transcription	HSMM	muscle
36	chr4:56042600-56042800	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:56042600-56043800	Weak transcription	Right Atrium	heart
38	chr4:56042600-56046800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:56042600-56047200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:56042600-56047200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:56042600-56047200	Weak transcription	Osteobl	bone
42	chr4:56042600-56047400	Weak transcription	NHLF	lung
43	chr4:56042600-56050600	Weak transcription	Placenta	Placenta

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