Variant report

Variant	rs55979571
Chromosome Location	chr18:12200651-12200652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr18:12200105-12200720	K562	blood:	n/a	n/a
2	NFIC	chr18:12199775-12200655	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000267733	TF binding region
ENSG00000267643	TF binding region

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10445425	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10445426	0.82[EUR][1000 genomes]
rs11080549	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11080550	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11877166	0.86[EUR][1000 genomes]
rs12604417	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12605170	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12605187	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12605231	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12607481	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12955316	0.81[EUR][1000 genomes]
rs12963518	0.87[EUR][1000 genomes]
rs12965571	0.82[EUR][1000 genomes]
rs12969917	0.81[EUR][1000 genomes]
rs2276370	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2851905	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2851907	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851923	0.85[EUR][1000 genomes]
rs28592744	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28648884	0.85[EUR][1000 genomes]
rs34036584	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34185303	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4239305	0.85[EUR][1000 genomes]
rs4261610	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4296321	0.88[EUR][1000 genomes]
rs4299212	0.88[EUR][1000 genomes]
rs4303617	0.88[EUR][1000 genomes]
rs4306582	0.88[EUR][1000 genomes]
rs4327115	0.86[EUR][1000 genomes]
rs4337367	0.88[EUR][1000 genomes]
rs4347689	0.82[EUR][1000 genomes]
rs4402627	0.88[EUR][1000 genomes]
rs4416083	0.81[EUR][1000 genomes]
rs4419117	0.81[EUR][1000 genomes]
rs4452021	0.83[EUR][1000 genomes]
rs4456573	0.88[EUR][1000 genomes]
rs4462671	0.85[EUR][1000 genomes]
rs4464145	0.88[EUR][1000 genomes]
rs4480870	0.88[EUR][1000 genomes]
rs4519391	0.81[EUR][1000 genomes]
rs4528645	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4528648	0.82[EUR][1000 genomes]
rs4538071	0.85[EUR][1000 genomes]
rs4569357	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4572475	0.88[EUR][1000 genomes]
rs4583319	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4621045	0.81[EUR][1000 genomes]
rs4796946	0.80[EUR][1000 genomes]
rs4796947	0.82[EUR][1000 genomes]
rs4797623	0.80[EUR][1000 genomes]
rs4797624	0.85[EUR][1000 genomes]
rs4797625	0.84[EUR][1000 genomes]
rs4797631	0.88[EUR][1000 genomes]
rs4797632	0.87[EUR][1000 genomes]
rs4797633	0.88[EUR][1000 genomes]
rs4797634	0.88[EUR][1000 genomes]
rs4797636	0.88[EUR][1000 genomes]
rs4797637	0.88[EUR][1000 genomes]
rs4797640	0.85[EUR][1000 genomes]
rs56101236	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57801464	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60010024	0.82[EUR][1000 genomes]
rs60311032	0.83[AMR][1000 genomes]
rs60401418	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61343100	0.83[AMR][1000 genomes]
rs61606757	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62097608	0.84[EUR][1000 genomes]
rs62097613	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62099061	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62099085	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6505717	0.81[EUR][1000 genomes]
rs6505720	0.87[EUR][1000 genomes]
rs6505725	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7226400	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7227857	0.87[EUR][1000 genomes]
rs7237912	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7239346	0.85[EUR][1000 genomes]
rs7239448	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7239947	0.87[EUR][1000 genomes]
rs7240093	0.85[EUR][1000 genomes]
rs7242541	0.80[EUR][1000 genomes]
rs7243248	0.85[EUR][1000 genomes]
rs7244723	0.81[EUR][1000 genomes]
rs73410960	0.88[EUR][1000 genomes]
rs8082868	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8082888	0.87[EUR][1000 genomes]
rs8084532	0.81[AMR][1000 genomes]
rs8087637	0.88[EUR][1000 genomes]
rs8091463	0.81[EUR][1000 genomes]
rs8091585	0.81[EUR][1000 genomes]
rs8093417	0.80[EUR][1000 genomes]
rs8095234	0.80[EUR][1000 genomes]
rs8095647	0.80[EUR][1000 genomes]
rs8098332	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8099792	0.82[EUR][1000 genomes]
rs9303759	0.85[EUR][1000 genomes]
rs9303760	0.84[EUR][1000 genomes]
rs9945491	0.87[EUR][1000 genomes]
rs9948384	0.80[EUR][1000 genomes]
rs9951904	0.84[EUR][1000 genomes]
rs9953892	0.87[EUR][1000 genomes]
rs9954852	0.85[EUR][1000 genomes]
rs9954861	0.85[EUR][1000 genomes]
rs9954884	0.86[EUR][1000 genomes]
rs9955629	0.87[EUR][1000 genomes]
rs9956465	0.81[EUR][1000 genomes]
rs9956997	0.81[EUR][1000 genomes]
rs9957303	0.81[EUR][1000 genomes]
rs9959641	0.81[EUR][1000 genomes]
rs9963587	0.82[EUR][1000 genomes]
rs9965004	0.82[EUR][1000 genomes]
rs9965108	0.85[EUR][1000 genomes]
rs9966965	0.83[EUR][1000 genomes]
rs9967372	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv1055343	chr18:12107012-12226356	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv960252	chr18:12161216-12220798	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55979571	RP11-64C12.3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12198800-12201000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr18:12199000-12200800	Enhancers	GM12878-XiMat	blood
3	chr18:12199000-12201000	Enhancers	Primary B cells from peripheral blood	blood
4	chr18:12199600-12200800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr18:12199800-12201000	Enhancers	K562	blood
6	chr18:12200600-12202000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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