Variant report

Variant	rs4954352
Chromosome Location	chr2:133409670-133409671
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:133406755..133409738-chr2:133422944..133424872,2	MCF-7	breast:
2	chr2:133408258..133410469-chr2:133426160..133428475,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150551	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10179167	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10179785	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10189715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1131671	0.92[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs13028563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430630	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1430631	0.86[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs1430632	0.86[CHB][hapmap];0.96[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17396523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17396537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17396607	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1897166	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2082177	0.83[ASN][1000 genomes]
rs2082179	0.88[ASN][1000 genomes]
rs2082181	0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2163342	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2244888	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2248193	0.87[ASN][1000 genomes]
rs2288653	0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2315521	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2315599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2320153	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2435612	0.86[CHB][hapmap];0.96[JPT][hapmap];0.97[ASN][1000 genomes]
rs2566528	0.85[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs2566529	0.87[ASN][1000 genomes]
rs2566530	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2566531	0.81[JPT][hapmap]
rs2566535	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2566536	0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2566537	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2566538	0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2709520	0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2709521	0.87[ASN][1000 genomes]
rs2709523	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2709524	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2709525	0.86[CHB][hapmap];0.96[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2709526	0.95[ASN][1000 genomes]
rs2709527	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2709528	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2709532	0.87[ASN][1000 genomes]
rs2709533	0.89[ASN][1000 genomes]
rs2709545	0.84[ASN][1000 genomes]
rs2709546	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2709548	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2709549	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3738842	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4340582	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4547578	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4954351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6430370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs713535	0.86[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs721470	0.87[ASN][1000 genomes]
rs744821	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7558213	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7558730	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7567602	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7603894	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7603926	0.88[ASN][1000 genomes]
rs7608591	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9973717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133390200-133412600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:133390400-133413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:133390400-133423800	Weak transcription	A549	lung
4	chr2:133399800-133410800	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:133403000-133419600	Weak transcription	Fetal Kidney	kidney
6	chr2:133404000-133410000	Weak transcription	Fetal Stomach	stomach
7	chr2:133404000-133411400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:133404000-133413800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:133404000-133426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:133404200-133412600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:133404400-133413600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:133404600-133410200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:133404600-133413600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:133404800-133409800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:133408000-133410400	Enhancers	Brain Anterior Caudate	brain
16	chr2:133409200-133411000	Weak transcription	HUVEC	blood vessel
17	chr2:133409400-133409800	Flanking Active TSS	Osteobl	bone
18	chr2:133409400-133410200	Enhancers	Brain Substantia Nigra	brain
19	chr2:133409400-133410200	Enhancers	Lung	lung
20	chr2:133409400-133410800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:133409400-133411000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:133409600-133410000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:133409600-133410000	Enhancers	Brain Germinal Matrix	brain
24	chr2:133409600-133410400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:133409600-133410800	Weak transcription	Fetal Brain Female	brain
26	chr2:133409600-133411000	Enhancers	NH-A	brain
27	chr2:133409600-133411200	Weak transcription	Fetal Brain Male	brain
28	chr2:133409600-133412200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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