Variant report

Variant	rs4902259
Chromosome Location	chr14:39419283-39419284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10134230	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10134654	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137988	0.95[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10140949	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10141255	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10141471	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11157041	0.83[CEU][hapmap];0.88[CHD][hapmap];0.89[MEX][hapmap];0.87[AMR][1000 genomes]
rs12050319	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12434593	0.82[ASN][1000 genomes]
rs12434847	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437031	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437346	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878139	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12878789	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879229	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12882868	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12885242	0.80[CEU][hapmap];0.91[CHD][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes]
rs12890771	0.95[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555257	0.91[CHD][hapmap]
rs17108728	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1957064	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2025064	0.82[ASN][1000 genomes]
rs2415522	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28367031	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34676226	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34985331	0.86[AMR][1000 genomes]
rs35287240	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35712728	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35807641	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36161173	0.87[AMR][1000 genomes]
rs3742354	0.80[CEU][hapmap];0.84[CHD][hapmap];0.89[MEX][hapmap]
rs3742355	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4902308	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71407775	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7150092	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7151246	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7152746	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs9322992	0.85[CEU][hapmap];0.87[AMR][1000 genomes]
rs9743575	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs975521	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv564416	chr14:39140536-39440106	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv470631	chr14:39153764-39440106	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv901656	chr14:39370726-39423339	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv901657	chr14:39410706-39460072	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4902259	FIBP	trans	parietal	SCAN
rs4902259	TRAPPC6B	cis	cerebellum	SCAN
rs4902259	TRAPPC6B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39414200-39433600	Weak transcription	Brain Angular Gyrus	brain
2	chr14:39417800-39420400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr14:39417800-39420600	Weak transcription	NH-A	brain
4	chr14:39417800-39421000	Weak transcription	Osteobl	bone
5	chr14:39418000-39419800	Weak transcription	HUVEC	blood vessel
6	chr14:39418000-39420000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr14:39418000-39420000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr14:39418000-39420400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr14:39418000-39420600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr14:39418000-39420600	Weak transcription	HSMM	muscle
11	chr14:39418000-39420800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr14:39418000-39428000	Weak transcription	Brain Hippocampus Middle	brain
13	chr14:39418200-39419400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr14:39418400-39421000	Weak transcription	Brain Substantia Nigra	brain
15	chr14:39419200-39420200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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