Variant report

Variant	rs13005638
Chromosome Location	chr2:211348297-211348298
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10184506	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10195425	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10932336	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10932340	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12694200	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1509816	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1858194	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1858195	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2160851	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2287426	0.85[EUR][1000 genomes]
rs2287427	0.85[EUR][1000 genomes]
rs2370962	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2664239	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34374637	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35003355	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3732058	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3755185	0.83[EUR][1000 genomes]
rs3755186	0.83[EUR][1000 genomes]
rs3755187	0.82[EUR][1000 genomes]
rs3770686	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3770688	0.85[EUR][1000 genomes]
rs3770693	0.85[EUR][1000 genomes]
rs3770696	0.83[EUR][1000 genomes]
rs3845634	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4672580	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4672581	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4672582	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57718949	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6749711	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6752530	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7590759	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs759688	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs759689	0.88[EUR][1000 genomes];0.97[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	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13005638	LANCL1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211341600-211348800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:211341600-211348800	Weak transcription	Pancreas	Pancrea
3	chr2:211343000-211355200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:211343400-211363600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:211344000-211348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:211344000-211350800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:211345600-211349600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:211347000-211348800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:211348000-211348400	Enhancers	Ovary	ovary

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