Variant report

Variant	rs2566538
Chromosome Location	chr2:133416865-133416866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr2:133416668-133416935	HepG2	liver:	n/a	chr2:133416676-133416692 chr2:133416845-133416856 chr2:133416680-133416691 chr2:133416846-133416857 chr2:133416679-133416693 chr2:133416846-133416857 chr2:133416841-133416857 chr2:133416680-133416691
2	MAFK	chr2:133416670-133417003	IMR90	lung:	n/a	chr2:133416676-133416692 chr2:133416845-133416856 chr2:133416680-133416691 chr2:133416846-133416857 chr2:133416679-133416693 chr2:133416846-133416857 chr2:133416841-133416857 chr2:133416680-133416691
3	MAFF	chr2:133416674-133416966	HepG2	liver:	n/a	chr2:133416840-133416858
4	MAFK	chr2:133416665-133417004	HepG2	liver:	n/a	chr2:133416676-133416692 chr2:133416845-133416856 chr2:133416680-133416691 chr2:133416846-133416857 chr2:133416679-133416693 chr2:133416846-133416857 chr2:133416841-133416857 chr2:133416680-133416691

Variant related genes	Relation type
ENSG00000230065	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10179167	0.87[ASN][1000 genomes]
rs10179785	0.92[ASN][1000 genomes]
rs10189715	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1131671	0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs13028563	0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1430630	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1430632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396523	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17396537	0.86[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs17396607	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1897166	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2033332	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2082177	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2082179	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2082181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2163342	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244888	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2248193	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2315599	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2320153	0.92[ASN][1000 genomes]
rs2435612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2566525	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2566528	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2566529	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2566530	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2566531	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2566535	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2566536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2566537	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2709520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2709521	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2709523	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2709524	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2709525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709526	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709527	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2709528	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2709532	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2709533	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2709534	0.84[CEU][hapmap];0.95[EUR][1000 genomes]
rs2709536	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2709541	0.82[EUR][1000 genomes]
rs2709542	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2709545	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2709546	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2709548	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2709549	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3738842	0.92[ASN][1000 genomes]
rs4340582	0.92[ASN][1000 genomes]
rs4547578	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4954351	0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4954352	0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6430370	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs713535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs721470	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs744821	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7558213	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7558730	0.88[ASN][1000 genomes]
rs7567602	0.88[ASN][1000 genomes]
rs7603894	0.88[ASN][1000 genomes]
rs7603926	0.85[ASN][1000 genomes]
rs7608591	0.88[ASN][1000 genomes]
rs9973717	0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[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	nsv1011421	chr2:132895241-133682185	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv875137	chr2:133167263-133714142	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription 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	13 gene(s)	inside rSNPs	diseases
3	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv875138	chr2:133410921-133761794	Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133390400-133423800	Weak transcription	A549	lung
2	chr2:133403000-133419600	Weak transcription	Fetal Kidney	kidney
3	chr2:133404000-133426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:133410000-133426200	Weak transcription	Osteobl	bone
5	chr2:133412200-133424400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:133413400-133418600	Enhancers	Brain Anterior Caudate	brain
7	chr2:133414000-133420400	Weak transcription	NHLF	lung
8	chr2:133414200-133422400	Strong transcription	HUVEC	blood vessel
9	chr2:133414200-133426000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:133414400-133417600	Enhancers	Brain Cingulate Gyrus	brain
11	chr2:133414400-133419800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:133414400-133420400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:133414600-133424000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:133414800-133419600	Strong transcription	NH-A	brain
15	chr2:133415000-133421400	Weak transcription	Brain Germinal Matrix	brain
16	chr2:133415200-133418600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:133415600-133417400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:133415800-133417400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:133415800-133417600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:133415800-133421000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:133416000-133419200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:133416200-133417400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr2:133416200-133417400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:133416400-133417400	Enhancers	Fetal Brain Male	brain
25	chr2:133416400-133417800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr2:133416400-133418200	Enhancers	Brain Substantia Nigra	brain
27	chr2:133416600-133417800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:133416600-133418000	Enhancers	Brain Hippocampus Middle	brain
29	chr2:133416800-133417800	Enhancers	Brain Angular Gyrus	brain

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