Variant report

Variant	rs12499210
Chromosome Location	chr4:100088567-100088568
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:51)

rs_ID	r²[population]
rs10022174	0.92[EUR][1000 genomes]
rs10026860	0.92[EUR][1000 genomes]
rs12499710	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12501204	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12502056	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12504321	0.84[EUR][1000 genomes]
rs12504365	0.84[EUR][1000 genomes]
rs12504491	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12505816	0.82[EUR][1000 genomes]
rs12506882	0.86[EUR][1000 genomes]
rs12507078	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12508502	0.84[EUR][1000 genomes]
rs12512053	0.84[EUR][1000 genomes]
rs12512110	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12649136	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16996598	1.00[ASN][1000 genomes]
rs17028765	0.86[EUR][1000 genomes]
rs17033	0.81[EUR][1000 genomes]
rs2010612	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2156731	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2226896	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2276332	0.84[EUR][1000 genomes]
rs28364333	0.84[EUR][1000 genomes]
rs28914770	0.81[EUR][1000 genomes]
rs28914775	0.81[EUR][1000 genomes]
rs28914794	0.81[EUR][1000 genomes]
rs35882815	0.92[EUR][1000 genomes]
rs36139400	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805325	0.84[EUR][1000 genomes]
rs4148884	0.92[EUR][1000 genomes]
rs4699381	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4699734	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55926943	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57058570	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57428460	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58660705	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58827689	0.86[EUR][1000 genomes]
rs58964688	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60345995	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60468511	0.84[EUR][1000 genomes]
rs61681818	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840413	0.91[EUR][1000 genomes]
rs72679827	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72679867	0.89[EUR][1000 genomes]
rs72679874	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72679893	0.82[EUR][1000 genomes]
rs7654607	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7663369	0.85[EUR][1000 genomes]
rs7669335	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7692358	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7692974	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3528915	chr4:100025155-100096234	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3528916	chr4:100025155-100096234	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3355763	chr4:100070566-100376814	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv879657	chr4:100082154-100139366	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100035000-100098200	Weak transcription	Ovary	ovary
2	chr4:100065600-100096600	Weak transcription	Fetal Lung	lung
3	chr4:100072200-100101400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:100082800-100101200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:100083000-100098200	Weak transcription	Aorta	Aorta
6	chr4:100086400-100090400	Enhancers	Liver	Liver
7	chr4:100087000-100089600	Enhancers	HepG2	liver
8	chr4:100088000-100088600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:100088400-100088600	Enhancers	Pancreas	Pancrea
10	chr4:100088400-100089200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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