Variant report

Variant	rs2682054
Chromosome Location	chr15:56547148-56547149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56533157..56539020-chr15:56544541..56548879,7	K562	blood:

Variant related genes	Relation type
ENSG00000151575	Chromatin interaction
ENSG00000181827	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11629483	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11630363	0.96[CEU][hapmap]
rs11631191	0.87[EUR][1000 genomes]
rs12900678	0.96[CEU][hapmap]
rs12905782	0.92[CEU][hapmap]
rs12905899	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12911094	0.92[CEU][hapmap]
rs12911427	0.96[CEU][hapmap]
rs12914640	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1372753	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1477590	0.89[CEU][hapmap]
rs1549452	1.00[CEU][hapmap]
rs17819438	1.00[CEU][hapmap]
rs1829542	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2119937	0.92[CEU][hapmap]
rs2249090	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs2303441	1.00[CEU][hapmap]
rs2414464	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2460647	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2460648	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2460650	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2682044	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682046	0.85[EUR][1000 genomes]
rs2682049	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682051	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2682053	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2682059	0.96[CEU][hapmap]
rs2713923	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2713924	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2713926	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2713931	0.83[AMR][1000 genomes]
rs2713933	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2713935	0.82[CEU][hapmap];0.97[ASN][1000 genomes]
rs2713936	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2713938	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2713941	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2718915	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2718934	1.00[CEU][hapmap]
rs2718941	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2725854	0.96[CEU][hapmap];0.82[AMR][1000 genomes]
rs2725870	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2947021	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs35749329	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35972806	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3784552	0.96[CEU][hapmap]
rs3817406	0.96[CEU][hapmap]
rs4310791	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4310792	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4774232	1.00[CEU][hapmap]
rs59432349	0.87[EUR][1000 genomes]
rs62044110	0.80[EUR][1000 genomes]
rs62044111	0.80[EUR][1000 genomes]
rs6493856	0.96[CEU][hapmap]
rs6493858	0.96[CEU][hapmap]
rs7170307	0.89[CEU][hapmap]
rs7174823	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7176107	0.80[CEU][hapmap]
rs7496025	1.00[CEU][hapmap]
rs8024031	0.92[CEU][hapmap]
rs9672886	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9672928	0.82[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	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2682054	RFX7	cis	Adipose Subcutaneous	GTEx
rs2682054	FLJ12994	cis	multi-tissue	Pritchard
rs2682054	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs2682054	RFXDC2	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56546800-56548000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:56547000-56547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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