Variant report

Variant	rs2370962
Chromosome Location	chr2:211370130-211370131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10184506	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10195425	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs10515951	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10932336	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10932340	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12694200	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13005638	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13013076	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs1509816	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858194	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2160851	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2287426	1.00[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2287427	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2664239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34374637	0.85[AMR][1000 genomes]
rs35003355	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3732058	1.00[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3755186	1.00[CEU][hapmap]
rs3755187	1.00[CEU][hapmap]
rs3770686	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3770688	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs3770693	1.00[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3770696	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs3845634	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4640325	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4672580	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4672581	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4672582	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57718949	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62203712	0.87[ASN][1000 genomes]
rs6749711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6752530	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7590759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs759688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs759689	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs918234	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9941507	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]

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
rs2370962	LANCL1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211364200-211370200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:211368600-211370200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:211368600-211370200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:211369000-211370200	Enhancers	Brain Cingulate Gyrus	brain
5	chr2:211369200-211370800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr2:211369400-211370200	Enhancers	HepG2	liver
7	chr2:211369600-211370400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
8	chr2:211369800-211370200	Enhancers	Brain Hippocampus Middle	brain
9	chr2:211370000-211370200	Active TSS	Brain Substantia Nigra	brain

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