Variant report

Variant	rs1449302
Chromosome Location	chr3:100729651-100729652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10936459	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10936460	0.87[ASN][1000 genomes]
rs10936464	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs13062274	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066740	0.87[ASN][1000 genomes]
rs13072542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075849	0.87[ASN][1000 genomes]
rs13079773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080505	0.87[ASN][1000 genomes]
rs13082728	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090397	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091963	0.85[ASN][1000 genomes]
rs1449300	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449305	0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1449315	0.86[ASN][1000 genomes]
rs1449320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843113	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16843116	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16843148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843163	0.87[ASN][1000 genomes]
rs1965214	0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2254374	0.86[ASN][1000 genomes]
rs2595904	0.90[ASN][1000 genomes]
rs2595914	0.86[ASN][1000 genomes]
rs2595917	0.86[ASN][1000 genomes]
rs2713757	1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2713768	0.85[ASN][1000 genomes]
rs2713769	0.85[ASN][1000 genomes]
rs2713770	0.88[ASN][1000 genomes]
rs2713771	0.86[ASN][1000 genomes]
rs2713773	0.85[ASN][1000 genomes]
rs2713774	0.86[ASN][1000 genomes]
rs2713775	0.86[ASN][1000 genomes]
rs2713776	0.86[ASN][1000 genomes]
rs28365990	0.87[ASN][1000 genomes]
rs2873448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34350012	0.86[ASN][1000 genomes]
rs34670326	0.87[ASN][1000 genomes]
rs34748077	0.85[ASN][1000 genomes]
rs35064087	0.86[ASN][1000 genomes]
rs35290466	0.86[ASN][1000 genomes]
rs3732895	0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3732896	0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3806655	0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41273569	0.87[ASN][1000 genomes]
rs4928060	0.87[ASN][1000 genomes]
rs4928102	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4928104	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs56847573	0.84[ASN][1000 genomes]
rs58004340	0.86[ASN][1000 genomes]
rs7631509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877222	chr3:100715576-101038297	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1449302	IFI44	trans	parietal	SCAN
rs1449302	TFG	cis	cerebellum	SCAN
rs1449302	PTBP2	trans	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100728200-100730000	Enhancers	Muscle Satellite Cultured Cells	--
2	chr3:100728200-100730000	Enhancers	HMEC	breast
3	chr3:100728200-100730600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:100728400-100730200	Enhancers	HSMM	muscle
5	chr3:100728400-100730200	Enhancers	NHEK	skin
6	chr3:100728800-100729800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:100728800-100730000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:100728800-100730000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:100728800-100730200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:100728800-100735600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:100729400-100730600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:100729600-100730000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:100729600-100730000	Flanking Active TSS	Osteobl	bone
14	chr3:100729600-100730600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:100729600-100730600	Flanking Active TSS	NHDF-Ad	bronchial

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