Variant report

Variant	rs1438551
Chromosome Location	chr3:105104247-105104248
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105102643..105105325-chr3:105235464..105238023,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12496827	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13065937	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13070223	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13070790	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13075944	0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs13077096	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13079517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13079993	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13085657	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13092913	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13095216	0.81[ASN][1000 genomes]
rs13095274	0.81[ASN][1000 genomes]
rs13095691	0.84[EUR][1000 genomes]
rs1438548	0.94[YRI][hapmap]
rs1438549	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16851097	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16851175	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2399046	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34198525	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35401795	0.90[AFR][1000 genomes]
rs35616213	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4894926	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4894928	0.85[EUR][1000 genomes]
rs6437582	0.81[ASN][1000 genomes]
rs6437583	0.81[ASN][1000 genomes]
rs6437584	0.81[ASN][1000 genomes]
rs66713063	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7431148	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7626665	0.81[ASN][1000 genomes]
rs976530	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105089000-105107000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:105090800-105104800	Weak transcription	NHLF	lung
3	chr3:105091400-105105000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:105091800-105104600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:105091800-105104800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:105092000-105106000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:105092800-105105200	Weak transcription	HMEC	breast
8	chr3:105094200-105105600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:105094400-105109000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:105095800-105104400	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:105097000-105106000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:105098000-105105200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:105102000-105104800	Weak transcription	Brain Anterior Caudate	brain
14	chr3:105103600-105104400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:105103600-105107000	Enhancers	Brain Substantia Nigra	brain
16	chr3:105103800-105104400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:105103800-105104800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:105103800-105105200	Enhancers	Osteobl	bone
19	chr3:105104000-105104400	Enhancers	NH-A	brain
20	chr3:105104000-105104600	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr3:105104000-105107600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr3:105104000-105108000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:105104200-105104400	Enhancers	GM12878-XiMat	blood
24	chr3:105104200-105104800	Active TSS	NHDF-Ad	bronchial
25	chr3:105104200-105105000	Enhancers	Aorta	Aorta
26	chr3:105104200-105105200	Flanking Active TSS	A549	lung
27	chr3:105104200-105105400	Enhancers	Brain Angular Gyrus	brain
28	chr3:105104200-105105800	Enhancers	NHEK	skin
29	chr3:105104200-105107000	Enhancers	Primary B cells from peripheral blood	blood
30	chr3:105104200-105107400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:105104200-105108000	Enhancers	HepG2	liver

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