Variant report

Variant	rs2566536
Chromosome Location	chr2:133421412-133421413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:133420207..133421735-chr2:133437928..133439428,2	MCF-7	breast:
2	chr2:133412910..133415477-chr2:133419851..133422133,2	MCF-7	breast:
3	chr2:133416681..133418753-chr2:133420029..133422139,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230065	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10179167	0.85[ASN][1000 genomes]
rs10179785	0.86[ASN][1000 genomes]
rs10189715	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1131671	0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs13028563	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1430630	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1430631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1430632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17396523	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17396537	0.86[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs17396607	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1897166	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033332	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs2082177	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2082179	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2082181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163342	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2244888	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2248193	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2315599	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2320153	0.85[ASN][1000 genomes]
rs2435612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2566525	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs2566528	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2566529	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2566530	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2566531	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2566535	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2566537	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2566538	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]
rs2709520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709521	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709523	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2709524	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2709525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2709526	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2709527	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2709528	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2709532	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709533	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2709534	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs2709536	0.87[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2709541	0.83[EUR][1000 genomes]
rs2709542	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs2709545	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2709546	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2709548	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2709549	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3738842	0.89[ASN][1000 genomes]
rs4340582	0.88[ASN][1000 genomes]
rs4547578	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4954351	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs4954352	0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs6430370	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs713535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs721470	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs744821	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7558213	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7558730	0.86[ASN][1000 genomes]
rs7567602	0.86[ASN][1000 genomes]
rs7603894	0.86[ASN][1000 genomes]
rs7603926	0.83[ASN][1000 genomes]
rs7608591	0.86[ASN][1000 genomes]
rs9973717	0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.89[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2566536	ANKRD30BL	cis	lymphoblastoid	seeQTL
rs2566536	UBXN4	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133390400-133423800	Weak transcription	A549	lung
2	chr2:133404000-133426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:133410000-133426200	Weak transcription	Osteobl	bone
4	chr2:133412200-133424400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:133414200-133422400	Strong transcription	HUVEC	blood vessel
6	chr2:133414200-133426000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:133414600-133424000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:133417400-133421600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:133417600-133425600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:133417800-133422600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:133418000-133423800	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:133418600-133425600	Weak transcription	Brain Anterior Caudate	brain
13	chr2:133419000-133424800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:133419200-133425200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:133419600-133421600	Weak transcription	NH-A	brain
16	chr2:133419800-133422400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:133420400-133422200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:133420800-133425200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:133421000-133423000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:133421400-133422000	Enhancers	Fetal Kidney	kidney
21	chr2:133421400-133423200	Enhancers	Brain Germinal Matrix	brain

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