Variant report

Variant	rs2403172
Chromosome Location	chr14:103834420-103834421
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12589817	0.87[ASN][1000 genomes]
rs17616316	1.00[CEU][hapmap]
rs17616464	1.00[CEU][hapmap]
rs2403171	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56982532	0.84[ASN][1000 genomes]
rs58153827	0.90[ASN][1000 genomes]
rs62006258	0.91[ASN][1000 genomes]
rs6575977	0.83[ASN][1000 genomes]
rs6575979	0.90[ASN][1000 genomes]
rs7149169	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7149827	0.86[EUR][1000 genomes]
rs7155749	1.00[CEU][hapmap]
rs8013228	0.89[ASN][1000 genomes]
rs8014669	0.84[ASN][1000 genomes]
rs959083	0.83[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	nsv1042714	chr14:103085298-103860730	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1049747	chr14:103126148-103955984	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
3	nsv534254	chr14:103470073-104023906	Bivalent Enhancer Enhancers Active TSS Weak transcription 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 miRNA target site	125 gene(s)	inside rSNPs	diseases
4	nsv9168	chr14:103531729-103913306	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2403172	BAG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103828400-103838600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr14:103831200-103838200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr14:103834000-103834800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr14:103834000-103835000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr14:103834200-103834600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr14:103834200-103834600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr14:103834200-103835000	Enhancers	NHLF	lung
8	chr14:103834400-103834600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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