Variant report

Variant	rs3853202
Chromosome Location	chr5:95906139-95906140
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10054767	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10062719	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1459839	0.81[ASN][1000 genomes]
rs149449	0.94[ASN][1000 genomes]
rs17086305	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs187819	0.86[ASN][1000 genomes]
rs2570462	0.84[ASN][1000 genomes]
rs2570464	0.82[ASN][1000 genomes]
rs2578697	0.93[ASN][1000 genomes]
rs2611727	0.86[ASN][1000 genomes]
rs261229	0.89[ASN][1000 genomes]
rs261230	0.89[ASN][1000 genomes]
rs261233	0.87[ASN][1000 genomes]
rs263378	0.85[ASN][1000 genomes]
rs263380	0.86[ASN][1000 genomes]
rs263381	0.86[ASN][1000 genomes]
rs4869294	0.80[JPT][hapmap]
rs66522472	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6868440	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881449	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[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	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1026484	chr5:95759910-95961518	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3853202	FAM172A	cis	cerebellum	SCAN
rs3853202	FAM172A	cis	parietal	SCAN
rs3853202	SPPL3	trans	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95902000-95908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:95903200-95906200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:95903200-95907400	Weak transcription	NHLF	lung
4	chr5:95903200-95908200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:95903200-95908400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:95903400-95908200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:95903400-95908200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:95903400-95908200	Weak transcription	HMEC	breast
9	chr5:95903400-95908200	Weak transcription	NHEK	skin
10	chr5:95903400-95908400	Weak transcription	NHDF-Ad	bronchial
11	chr5:95903600-95906200	Enhancers	HUVEC	blood vessel
12	chr5:95903600-95908400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:95903600-95908400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:95903800-95906800	Weak transcription	Hela-S3	cervix
15	chr5:95903800-95908400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:95903800-95908400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:95904200-95906400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:95905000-95907200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:95905400-95918200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:95905800-95908400	Weak transcription	HSMM	muscle
21	chr5:95906000-95907400	Weak transcription	NH-A	brain
22	chr5:95906000-95908400	Weak transcription	A549	lung
23	chr5:95906000-95908400	Weak transcription	Osteobl	bone

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