Variant report

Variant	rs10002599
Chromosome Location	chr4:82107777-82107778
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10003341	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10005912	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10006560	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10516650	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11099460	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11722020	0.83[EUR][1000 genomes]
rs11933194	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11941219	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12330930	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12331759	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12331821	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12331945	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12332035	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12643702	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1517547	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1545287	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1546651	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1972127	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28413060	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28419569	0.82[AMR][1000 genomes]
rs28445932	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28491787	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28508156	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28669195	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2868141	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28782932	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28783134	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28844140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903751	0.88[AMR][1000 genomes]
rs3943629	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56008646	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56061857	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56845428	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59441619	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59896344	0.83[EUR][1000 genomes]
rs60111302	0.83[EUR][1000 genomes]
rs60138132	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60510576	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60808851	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6811913	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6828114	0.83[EUR][1000 genomes]
rs6842611	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6857403	0.81[AMR][1000 genomes]
rs72879491	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72879493	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72879502	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72880604	0.83[EUR][1000 genomes]
rs72881305	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7659331	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7680521	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7687258	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs984924	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs986290	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9990953	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9990963	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9994631	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829984	chr4:81979988-82113977	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv1822437	chr4:82025743-82118996	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82088000-82113800	Weak transcription	Fetal Intestine Large	intestine
2	chr4:82088200-82114400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:82093600-82115400	Weak transcription	NHDF-Ad	bronchial
4	chr4:82100000-82117200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:82105600-82113400	Weak transcription	Fetal Intestine Small	intestine
6	chr4:82105600-82117200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:82106200-82115200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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