Variant report

Variant	rs2709525
Chromosome Location	chr2:133413072-133413073
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:133412013..133414888-chr2:133417480..133419360,2	MCF-7	breast:
2	chr2:133412910..133415477-chr2:133419851..133422133,2	MCF-7	breast:
3	chr2:133412628..133415708-chr2:133426870..133429537,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230065	Chromatin interaction
ENSG00000150551	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10179167	0.85[ASN][1000 genomes]
rs10179785	0.90[ASN][1000 genomes]
rs10189715	0.86[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1131671	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs13028563	0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1430630	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1430631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1430632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17396523	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17396537	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs17396607	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1897166	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2033332	0.88[CEU][hapmap]
rs2082177	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2082179	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2082181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2163342	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2244888	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2248193	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2288653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2315599	0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2320153	0.90[ASN][1000 genomes]
rs2435612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2566525	0.88[CEU][hapmap]
rs2566528	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2566529	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2566530	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2566531	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2566535	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2566536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2566537	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2566538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2709521	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2709523	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2709524	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709526	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2709527	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709528	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2709532	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2709533	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2709534	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2709536	0.87[CEU][hapmap]
rs2709542	0.88[CEU][hapmap]
rs2709545	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2709546	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2709548	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2709549	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3738842	0.90[ASN][1000 genomes]
rs4340582	0.89[ASN][1000 genomes]
rs4547578	0.87[ASN][1000 genomes]
rs4954351	0.86[CHB][hapmap];0.96[JPT][hapmap];0.94[ASN][1000 genomes]
rs4954352	0.86[CHB][hapmap];0.96[JPT][hapmap];0.82[AMR][1000 genomes];0.95[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];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs721470	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs744821	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558213	0.92[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];0.95[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv583155	chr2:133253386-133415170	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133390400-133413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:133390400-133423800	Weak transcription	A549	lung
3	chr2:133403000-133419600	Weak transcription	Fetal Kidney	kidney
4	chr2:133404000-133413800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:133404000-133426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:133404400-133413600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:133404600-133413600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:133410000-133413800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:133410000-133414200	Weak transcription	Brain Germinal Matrix	brain
10	chr2:133410000-133426200	Weak transcription	Osteobl	bone
11	chr2:133410400-133414000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:133410600-133413400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:133410800-133413800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:133411000-133414800	Weak transcription	NH-A	brain
15	chr2:133411600-133416000	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:133411800-133413400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:133411800-133413800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:133412000-133413400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:133412200-133413400	Weak transcription	Brain Anterior Caudate	brain
20	chr2:133412200-133413800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:133412200-133414000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:133412200-133414200	Weak transcription	HUVEC	blood vessel
23	chr2:133412200-133416400	Weak transcription	Brain Substantia Nigra	brain
24	chr2:133412200-133416800	Weak transcription	Brain Angular Gyrus	brain
25	chr2:133412200-133424400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:133412800-133413600	Weak transcription	NHLF	lung
27	chr2:133413000-133414600	Enhancers	Fetal Brain Male	brain

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