Variant report

Variant	rs10778375
Chromosome Location	chr12:105660998-105660999
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105660954..105663749-chr12:105664178..105665747,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10778374	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1109432	0.86[ASN][1000 genomes]
rs11112414	0.91[JPT][hapmap]
rs11112436	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196750	0.82[JPT][hapmap]
rs1196766	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1196767	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1196768	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1196776	0.86[ASN][1000 genomes]
rs1196778	0.85[ASN][1000 genomes]
rs1196779	0.85[ASN][1000 genomes]
rs1196781	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1196785	0.85[ASN][1000 genomes]
rs1196788	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1196796	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1196804	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1196812	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1196814	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1196816	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1196836	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1196838	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1196840	0.87[JPT][hapmap]
rs1196865	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1201657	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1201658	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs17036869	0.82[CHB][hapmap]
rs1732378	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1732384	0.86[JPT][hapmap]
rs2264066	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2374448	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2440708	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2440713	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2440717	0.86[JPT][hapmap]
rs2440719	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs4964130	0.84[ASN][1000 genomes]
rs4964348	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6539196	0.86[ASN][1000 genomes]
rs6539197	0.81[EUR][1000 genomes]
rs66925241	0.86[ASN][1000 genomes]
rs7134360	0.81[ASN][1000 genomes]
rs71441894	0.88[ASN][1000 genomes]
rs727888	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7309320	0.86[ASN][1000 genomes]
rs7310488	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9143	0.81[CHB][hapmap];0.86[JPT][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	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10778375	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL
rs10778375	APPL2	cis	cerebellar cortex	BrainEAC

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105652600-105661400	Weak transcription	HSMMtube	muscle
2	chr12:105653400-105661400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:105653400-105661400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:105656600-105661400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:105657200-105661800	Weak transcription	NHDF-Ad	bronchial
6	chr12:105659600-105672200	Weak transcription	Aorta	Aorta

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