Variant report

Variant	rs56020025
Chromosome Location	chr5:60349710-60349711
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10452451	0.83[AFR][1000 genomes]
rs16878535	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16878537	1.00[AMR][1000 genomes]
rs16878539	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16878544	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3910825	1.00[AMR][1000 genomes]
rs4647074	1.00[AMR][1000 genomes]
rs4647116	1.00[AMR][1000 genomes]
rs55638584	1.00[AMR][1000 genomes]
rs55659107	1.00[AMR][1000 genomes]
rs56043434	1.00[AMR][1000 genomes]
rs56071223	1.00[AMR][1000 genomes]
rs56113732	1.00[AMR][1000 genomes]
rs56132498	0.80[AFR][1000 genomes]
rs56256328	1.00[AMR][1000 genomes]
rs56287212	1.00[AMR][1000 genomes]
rs56306823	1.00[AMR][1000 genomes]
rs56320246	1.00[AMR][1000 genomes]
rs56386934	1.00[AMR][1000 genomes]
rs57108975	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57366470	1.00[AMR][1000 genomes]
rs58859855	0.94[AFR][1000 genomes]
rs58930565	1.00[AMR][1000 genomes]
rs59453232	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60239490	1.00[AMR][1000 genomes]
rs60328915	0.87[AFR][1000 genomes]
rs6449516	1.00[AMR][1000 genomes]
rs6860439	1.00[AMR][1000 genomes]
rs6869855	1.00[AMR][1000 genomes]
rs6870631	1.00[AMR][1000 genomes]
rs6881713	1.00[AMR][1000 genomes]
rs6881960	1.00[AMR][1000 genomes]
rs6885974	1.00[AMR][1000 genomes]
rs73759426	1.00[AMR][1000 genomes]
rs73759427	1.00[AMR][1000 genomes]
rs73759430	1.00[AMR][1000 genomes]
rs73759431	1.00[AMR][1000 genomes]
rs73759432	1.00[AMR][1000 genomes]
rs73759434	1.00[AMR][1000 genomes]
rs73759435	1.00[AMR][1000 genomes]
rs73759437	1.00[AMR][1000 genomes]
rs73759441	1.00[AMR][1000 genomes]
rs73759445	1.00[AMR][1000 genomes]
rs73759446	1.00[AMR][1000 genomes]
rs73759447	1.00[AMR][1000 genomes]
rs73759450	1.00[AMR][1000 genomes]
rs73759452	1.00[AMR][1000 genomes]
rs73759454	1.00[AMR][1000 genomes]
rs73759455	1.00[AMR][1000 genomes]
rs73759456	1.00[AMR][1000 genomes]
rs73759457	1.00[AMR][1000 genomes]
rs73759458	1.00[AMR][1000 genomes]
rs73759459	1.00[AMR][1000 genomes]
rs73759461	1.00[AMR][1000 genomes]
rs73759468	1.00[AMR][1000 genomes]
rs73759469	1.00[AMR][1000 genomes]
rs73759470	1.00[AMR][1000 genomes]
rs73759471	1.00[AMR][1000 genomes]
rs73759475	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73759487	0.87[AFR][1000 genomes]
rs7701959	1.00[AMR][1000 genomes]
rs7717284	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv881717	chr5:60141245-60372582	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv598313	chr5:60247815-60374912	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv881722	chr5:60266875-60384171	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1019307	chr5:60295350-60409077	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60324600-60354000	Weak transcription	Primary T cells from cord blood	blood
2	chr5:60326000-60400800	Weak transcription	Left Ventricle	heart
3	chr5:60344800-60353400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:60345600-60350800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:60346200-60350400	Enhancers	NHDF-Ad	bronchial
6	chr5:60346400-60350000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:60346400-60350200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:60346400-60350400	Enhancers	HMEC	breast
9	chr5:60346400-60350400	Enhancers	Osteobl	bone
10	chr5:60346600-60350400	Enhancers	NHEK	skin
11	chr5:60346800-60350400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:60346800-60350600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:60347000-60350000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:60347000-60350600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:60347200-60379200	Weak transcription	Ovary	ovary
16	chr5:60347400-60349800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:60347400-60351400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:60347400-60353000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:60347400-60356000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:60347800-60353000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:60348600-60350400	Enhancers	NHLF	lung
22	chr5:60349200-60350200	Weak transcription	NH-A	brain
23	chr5:60349200-60352800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:60349400-60350400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:60349400-60350400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr5:60349400-60350400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:60349400-60350400	Enhancers	A549	lung
28	chr5:60349400-60353000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:60349400-60370800	Weak transcription	HSMM	muscle
30	chr5:60349600-60353000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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