Variant report

Variant	rs12694200
Chromosome Location	chr2:211366879-211366880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10184506	0.80[EUR][1000 genomes]
rs10932336	0.88[ASN][1000 genomes]
rs10932340	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13005638	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1509816	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858194	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858195	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2160851	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2287426	0.80[EUR][1000 genomes]
rs2287427	0.80[EUR][1000 genomes]
rs2370962	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2664239	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35003355	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3732058	0.80[EUR][1000 genomes]
rs3770686	0.80[EUR][1000 genomes]
rs3770688	0.80[EUR][1000 genomes]
rs3770693	0.80[EUR][1000 genomes]
rs3845634	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672580	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4672581	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4672582	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57718949	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62203712	0.83[ASN][1000 genomes]
rs6749711	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6752530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7590759	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs759688	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs759689	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	esv3459962	chr2:211360526-211368951	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv3459963	chr2:211360858-211368614	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12694200	LANCL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211361400-211367400	Weak transcription	Brain Angular Gyrus	brain
2	chr2:211364200-211370200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:211364600-211367400	Weak transcription	Brain Anterior Caudate	brain
4	chr2:211364600-211367400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:211364600-211368000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:211364600-211368800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:211365000-211368200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:211365600-211367600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:211365600-211367800	Weak transcription	Fetal Intestine Large	intestine
10	chr2:211365800-211367800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:211365800-211368000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:211366000-211368000	Weak transcription	Stomach Mucosa	stomach
13	chr2:211366200-211367400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:211366200-211367400	Weak transcription	Hela-S3	cervix
15	chr2:211366800-211367400	Weak transcription	Ovary	ovary
16	chr2:211366800-211368000	Enhancers	Brain Substantia Nigra	brain

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