Variant report

Variant	rs12485790
Chromosome Location	chr3:142710351-142710352
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142295946..142298706-chr3:142708325..142711018,2	K562	blood:
2	chr3:142706036..142707865-chr3:142708223..142711029,2	K562	blood:
3	chr3:142645933..142648284-chr3:142709421..142711755,2	K562	blood:
4	chr3:142699207..142701682-chr3:142709605..142712109,2	K562	blood:

Variant related genes	Relation type
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10413	0.87[EUR][1000 genomes]
rs1043898	0.86[EUR][1000 genomes]
rs10451867	0.82[EUR][1000 genomes]
rs10513184	0.83[EUR][1000 genomes]
rs1053950	0.87[EUR][1000 genomes]
rs10790	0.81[EUR][1000 genomes]
rs10935475	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10935479	0.86[EUR][1000 genomes]
rs11915462	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11922201	0.89[EUR][1000 genomes]
rs12490776	0.82[EUR][1000 genomes]
rs12492904	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12695770	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13075955	0.82[EUR][1000 genomes]
rs13094293	0.85[EUR][1000 genomes]
rs1349262	0.87[EUR][1000 genomes]
rs13715	0.84[EUR][1000 genomes]
rs1375814	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1449868	0.90[EUR][1000 genomes]
rs1449869	0.87[EUR][1000 genomes]
rs1530753	0.87[EUR][1000 genomes]
rs1532588	0.88[EUR][1000 genomes]
rs1545597	0.87[EUR][1000 genomes]
rs17557029	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1814565	0.89[EUR][1000 genomes]
rs1827159	0.87[EUR][1000 genomes]
rs1839406	0.90[EUR][1000 genomes]
rs1868569	0.85[EUR][1000 genomes]
rs1868570	0.85[EUR][1000 genomes]
rs1965343	0.91[EUR][1000 genomes]
rs2045306	0.87[EUR][1000 genomes]
rs2124541	0.91[EUR][1000 genomes]
rs2124542	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2124543	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2137586	0.88[EUR][1000 genomes]
rs2175739	0.88[EUR][1000 genomes]
rs2290549	0.86[EUR][1000 genomes]
rs2353408	0.84[EUR][1000 genomes]
rs2353409	0.87[EUR][1000 genomes]
rs2353411	0.87[EUR][1000 genomes]
rs3821645	0.87[EUR][1000 genomes]
rs3856697	0.85[EUR][1000 genomes]
rs3902877	0.92[EUR][1000 genomes]
rs4030582	0.89[EUR][1000 genomes]
rs4683444	0.86[EUR][1000 genomes]
rs4683721	0.87[EUR][1000 genomes]
rs4683722	0.90[EUR][1000 genomes]
rs4683723	0.82[EUR][1000 genomes]
rs4683724	0.83[EUR][1000 genomes]
rs56382522	0.87[EUR][1000 genomes]
rs6440129	0.89[EUR][1000 genomes]
rs6440131	0.85[EUR][1000 genomes]
rs6440132	0.84[EUR][1000 genomes]
rs6440134	0.87[EUR][1000 genomes]
rs6770102	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6778454	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6781080	0.90[EUR][1000 genomes]
rs6781887	0.89[EUR][1000 genomes]
rs6783145	0.84[EUR][1000 genomes]
rs6802376	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6805417	0.86[EUR][1000 genomes]
rs6806551	0.85[EUR][1000 genomes]
rs6808689	0.90[EUR][1000 genomes]
rs7611721	0.90[EUR][1000 genomes]
rs7623532	0.86[EUR][1000 genomes]
rs7644475	0.82[EUR][1000 genomes]
rs7648143	0.85[EUR][1000 genomes]
rs7649225	0.81[EUR][1000 genomes]
rs7652745	0.82[EUR][1000 genomes]
rs766360	0.89[EUR][1000 genomes]
rs936194	0.87[EUR][1000 genomes]
rs936196	0.85[EUR][1000 genomes]
rs936197	0.82[EUR][1000 genomes]
rs937498	0.85[EUR][1000 genomes]
rs9814656	0.85[EUR][1000 genomes]
rs9816317	0.87[EUR][1000 genomes]
rs9835348	0.90[EUR][1000 genomes]
rs9847059	0.85[EUR][1000 genomes]
rs9851353	0.85[EUR][1000 genomes]
rs9862433	0.84[EUR][1000 genomes]
rs9877128	0.86[EUR][1000 genomes]
rs9877135	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12485790	SR140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142707000-142712000	Weak transcription	Liver	Liver
2	chr3:142707000-142712200	Weak transcription	K562	blood
3	chr3:142707000-142712600	Weak transcription	A549	lung
4	chr3:142707000-142715200	Weak transcription	Hela-S3	cervix
5	chr3:142707000-142716200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:142707000-142718800	Weak transcription	Right Ventricle	heart
7	chr3:142707200-142710600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:142710200-142718600	Weak transcription	GM12878-XiMat	blood

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