Variant report

Variant	rs62139199
Chromosome Location	chr2:54466223-54466224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54465360..54468834-chr2:54480824..54482850,3	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10165485	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10171249	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10175251	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10205866	0.85[ASN][1000 genomes]
rs11125529	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11890390	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11896604	0.95[EUR][1000 genomes]
rs12615749	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12615793	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12618994	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621747	0.85[ASN][1000 genomes]
rs12622470	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13411098	0.88[ASN][1000 genomes]
rs13423343	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13424638	0.85[ASN][1000 genomes]
rs17045711	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17045754	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1817557	0.88[ASN][1000 genomes]
rs1872329	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2062340	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28416696	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55635437	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56227395	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57060498	0.95[EUR][1000 genomes]
rs62139200	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62139251	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62139253	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62139254	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62139258	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62139259	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62140461	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6740641	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7579722	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1000652	chr2:54345892-54469703	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1009828	chr2:54393122-54488721	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv457897	chr2:54459093-54502912	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv582012	chr2:54459093-54502912	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54449800-54535200	Weak transcription	Primary T cells from cord blood	blood
2	chr2:54452400-54468000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:54452800-54490200	Weak transcription	Primary B cells from cord blood	blood
4	chr2:54455800-54476000	Weak transcription	K562	blood
5	chr2:54456400-54487200	Weak transcription	Psoas Muscle	Psoas
6	chr2:54461600-54466400	Weak transcription	Adipose Nuclei	Adipose
7	chr2:54465200-54467800	Weak transcription	Fetal Lung	lung
8	chr2:54465600-54467200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:54465800-54467600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:54466000-54468200	Enhancers	HSMM	muscle
11	chr2:54466000-54468400	Enhancers	HSMMtube	muscle
12	chr2:54466000-54468600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:54466000-54468600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:54466000-54468600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:54466000-54468600	Enhancers	Osteobl	bone
16	chr2:54466000-54468800	Enhancers	NHDF-Ad	bronchial
17	chr2:54466200-54466600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:54466200-54466600	Enhancers	Left Ventricle	heart
19	chr2:54466200-54466600	Enhancers	Right Ventricle	heart
20	chr2:54466200-54466600	Flanking Active TSS	NH-A	brain
21	chr2:54466200-54466800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:54466200-54467400	Enhancers	Ovary	ovary
23	chr2:54466200-54468000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:54466200-54468600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:54466200-54468600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr2:54466200-54468600	Enhancers	NHLF	lung
27	chr2:54466200-54468800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:54466200-54469400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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