Variant report

Variant	rs11925953
Chromosome Location	chr3:142796422-142796423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142795942..142800352-chr3:142837416..142841083,3	K562	blood:
2	chr3:142796365..142799329-chr3:142833969..142835708,2	K562	blood:
3	chr3:142791929..142795122-chr3:142795804..142797960,4	K562	blood:
4	chr3:142795942..142798929-chr3:142838470..142841083,3	K562	blood:
5	chr3:142794271..142797141-chr3:142844007..142845720,2	K562	blood:
6	chr3:142791929..142795122-chr3:142795804..142798158,4	K562	blood:

Variant related genes	Relation type
ENSG00000175040	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10935476	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11720696	0.87[AFR][1000 genomes]
rs11914346	0.83[EUR][1000 genomes]
rs11917259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11924590	0.84[EUR][1000 genomes]
rs11926643	0.80[EUR][1000 genomes]
rs11928485	0.81[EUR][1000 genomes]
rs13327838	0.80[EUR][1000 genomes]
rs1353887	0.85[JPT][hapmap]
rs1531139	0.96[CEU][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap]
rs16852909	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17557349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17633378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1869894	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124544	0.90[ASN][1000 genomes]
rs2173599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2353403	0.81[EUR][1000 genomes]
rs2353407	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41374546	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs4437106	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4616604	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55644607	0.82[EUR][1000 genomes]
rs56022259	0.80[EUR][1000 genomes]
rs56407378	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57654114	0.84[EUR][1000 genomes]
rs59510635	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60356687	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62276932	0.84[EUR][1000 genomes]
rs62276933	0.84[EUR][1000 genomes]
rs6781071	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73157700	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936198	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs9821734	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9846508	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1004467	chr3:142768867-142800605	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1004682	chr3:142768867-142804154	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11925953	U2SURP	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142793800-142797800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:142793800-142798000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:142794000-142798800	Weak transcription	K562	blood
4	chr3:142796200-142797600	Enhancers	Fetal Thymus	thymus
5	chr3:142796400-142797800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:142796400-142799000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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