Variant report

Variant	rs10742709
Chromosome Location	chr11:5555043-5555044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:5524283..5528575-chr11:5555009..5557870,6	K562	blood:
2	chr11:5523418..5528179-chr11:5553458..5558124,8	K562	blood:
3	chr11:5548734..5551432-chr11:5553725..5556576,3	K562	blood:

Variant related genes	Relation type
ENSG00000213931	Chromatin interaction
ENSG00000196565	Chromatin interaction
ENSG00000167355	Chromatin interaction
ENSG00000249633	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10160557	0.80[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs10160561	0.80[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10500648	0.92[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs10500649	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs10742708	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769042	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10769053	0.87[EUR][1000 genomes]
rs10769054	0.92[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs10838276	0.92[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs10838277	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs10838290	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs10838291	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs10838299	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs10838300	0.86[EUR][1000 genomes]
rs10838302	0.85[EUR][1000 genomes]
rs11037984	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs11037985	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs11037993	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11037994	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11038000	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11038004	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11038005	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11038048	0.86[EUR][1000 genomes]
rs12274305	0.90[EUR][1000 genomes]
rs12274861	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12275855	0.90[EUR][1000 genomes]
rs12288008	0.90[EUR][1000 genomes]
rs12294369	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12417988	0.90[EUR][1000 genomes]
rs12419693	0.90[EUR][1000 genomes]
rs12796126	0.90[EUR][1000 genomes]
rs1498480	0.94[EUR][1000 genomes]
rs1560811	0.94[EUR][1000 genomes]
rs182635	0.91[ASN][1000 genomes]
rs1846317	0.94[EUR][1000 genomes]
rs1995156	0.92[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs1995157	0.92[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs2201867	0.90[EUR][1000 genomes]
rs2201868	0.90[EUR][1000 genomes]
rs2879825	0.87[EUR][1000 genomes]
rs34822023	0.90[EUR][1000 genomes]
rs35601051	0.90[EUR][1000 genomes]
rs4910817	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs7103458	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs7120668	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7125746	0.90[EUR][1000 genomes]
rs7131305	0.88[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7944109	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048608	chr11:5328516-5645179	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
2	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv832057	chr11:5375585-5576200	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
4	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
6	nsv896940	chr11:5535007-5582430	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10742709	PHLDA2	cis	cerebellum	SCAN
rs10742709	KCNQ1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5554200-5556600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr11:5554400-5556000	Enhancers	K562	blood
3	chr11:5554600-5556600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:5555000-5555600	Enhancers	Primary neutrophils fromperipheralblood	blood

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