Variant report

Variant	rs6778460
Chromosome Location	chr3:105097427-105097428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2049217	1.00[JPT][hapmap]
rs62260776	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62262154	0.90[AFR][1000 genomes]
rs62263560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62263605	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62263606	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263608	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6437587	0.82[JPT][hapmap]
rs6764212	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];1.00[ASN][1000 genomes]
rs6804574	0.93[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73189010	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7621905	0.93[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9851952	0.82[JPT][hapmap]

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:26 , 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	chr3:105089200-105101800	Weak transcription	NHDF-Ad	bronchial
3	chr3:105090600-105101800	Weak transcription	Osteobl	bone
4	chr3:105090800-105104800	Weak transcription	NHLF	lung
5	chr3:105091000-105097600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:105091400-105105000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:105091600-105104000	Weak transcription	NH-A	brain
8	chr3:105091800-105104600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:105091800-105104800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:105092000-105097600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:105092000-105106000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:105092800-105100200	Weak transcription	NHEK	skin
13	chr3:105092800-105103600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:105092800-105104200	Weak transcription	HepG2	liver
15	chr3:105092800-105105200	Weak transcription	HMEC	breast
16	chr3:105093200-105103800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:105094200-105105600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:105094400-105109000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:105095000-105099000	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr3:105095400-105097800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:105095800-105104400	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:105097000-105097800	Weak transcription	A549	lung
23	chr3:105097000-105106000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:105097200-105098000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:105097400-105098000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:105097400-105098200	Enhancers	Brain Anterior Caudate	brain

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