Variant report

Variant	rs12129860
Chromosome Location	chr1:222153461-222153462
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11118926	0.86[EUR][1000 genomes]
rs12022676	0.89[ASN][1000 genomes]
rs12024555	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12025565	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12029332	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12032653	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032715	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12033415	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12121134	0.86[EUR][1000 genomes]
rs12125368	0.85[EUR][1000 genomes]
rs12125383	0.91[EUR][1000 genomes]
rs12140604	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12731064	0.86[EUR][1000 genomes]
rs12739936	0.86[EUR][1000 genomes]
rs17011182	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17011200	0.86[EUR][1000 genomes]
rs17442058	0.88[EUR][1000 genomes]
rs17442323	0.86[EUR][1000 genomes]
rs17495159	0.86[EUR][1000 genomes]
rs2095928	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35212520	0.86[EUR][1000 genomes]
rs35805428	0.86[EUR][1000 genomes]
rs56170536	0.85[EUR][1000 genomes]
rs66732677	0.85[EUR][1000 genomes]
rs6687758	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6691195	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6695584	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12129860	RP11-815M8.1	cis	lung	GTEx
rs12129860	RP11-400N13.2	cis	lung	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222146200-222163800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:222148800-222154800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:222152400-222156600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:222152600-222154600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr1:222152600-222157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:222152800-222156200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:222153000-222154200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:222153200-222161400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:222153200-222163800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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