Variant report

Variant	rs13080897
Chromosome Location	chr3:105207902-105207903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12488738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062434	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2399047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28588542	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4541433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6437595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6769329	0.86[CHB][hapmap]
rs6804472	0.86[CHB][hapmap]
rs7429428	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620022	0.84[CHB][hapmap]
rs7648171	0.90[YRI][hapmap]
rs9810954	0.85[ASN][1000 genomes]
rs9819036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9833101	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9833451	0.85[CHB][hapmap]
rs9843791	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9843918	0.85[ASN][1000 genomes]
rs9844458	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9857705	0.86[CHB][hapmap]
rs9857961	0.86[CHB][hapmap]
rs9863750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	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
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105193000-105209000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:105193000-105215400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:105193200-105209400	Weak transcription	HSMM	muscle
4	chr3:105193200-105209400	Weak transcription	NH-A	brain
5	chr3:105193200-105213600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:105200000-105209400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:105200000-105209400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:105201200-105214600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:105202800-105209400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:105204000-105209200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:105204600-105209400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:105205400-105213800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:105205600-105209000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:105207000-105209400	Weak transcription	Liver	Liver
15	chr3:105207400-105209400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:105207600-105209400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:105207600-105209600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:105207800-105208000	Enhancers	Brain Anterior Caudate	brain
19	chr3:105207800-105209600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:105207800-105209600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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