Variant report

Variant	rs11168413
Chromosome Location	chr12:48510995-48510996
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48510785..48513717-chr12:48592045..48593630,2	K562	blood:
2	chr12:48502266..48504790-chr12:48510214..48512208,2	K562	blood:

Variant related genes	Relation type
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10082861	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10219623	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10219645	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10467101	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs10875724	0.93[JPT][hapmap]
rs10875725	1.00[JPT][hapmap]
rs10875732	1.00[JPT][hapmap]
rs10875735	0.85[AMR][1000 genomes]
rs10875736	0.82[AMR][1000 genomes]
rs10875737	0.85[AMR][1000 genomes]
rs10875738	0.85[AMR][1000 genomes]
rs10875740	0.85[AMR][1000 genomes]
rs10875745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875746	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10875747	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875748	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10875756	0.90[ASN][1000 genomes]
rs10875762	0.81[ASN][1000 genomes]
rs10875767	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs10875770	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs10875772	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs10875792	0.85[JPT][hapmap]
rs10875793	0.92[JPT][hapmap]
rs11168357	0.93[JPT][hapmap]
rs11168369	1.00[JPT][hapmap]
rs11168371	1.00[JPT][hapmap]
rs11168383	0.85[AMR][1000 genomes]
rs11168386	0.83[AMR][1000 genomes]
rs11168401	0.85[AMR][1000 genomes]
rs11168403	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs11168414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11168415	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168416	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11168420	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168421	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168422	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11168425	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11168433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168450	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11168459	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs11168516	0.87[JPT][hapmap]
rs11558768	0.82[ASN][1000 genomes]
rs12297004	0.85[AMR][1000 genomes]
rs12297470	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12301339	0.85[AMR][1000 genomes]
rs12304476	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs12305182	0.93[JPT][hapmap]
rs12305511	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12306290	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12306451	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs12310813	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12311774	0.85[AMR][1000 genomes]
rs12311953	0.85[AMR][1000 genomes]
rs12312134	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12313300	0.85[AMR][1000 genomes]
rs12313404	0.83[AMR][1000 genomes]
rs12315625	0.85[AMR][1000 genomes]
rs17122620	0.85[AMR][1000 genomes]
rs17122666	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17122812	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1859445	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012773	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2079295	0.93[JPT][hapmap]
rs2107638	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2158516	0.85[AMR][1000 genomes]
rs2228500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2269933	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2269936	1.00[JPT][hapmap]
rs2279464	0.87[JPT][hapmap]
rs2286021	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3782910	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs3782911	0.85[AMR][1000 genomes]
rs4760609	0.93[JPT][hapmap]
rs4760619	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4760622	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4760680	0.85[AMR][1000 genomes]
rs4760681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4760684	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760687	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760689	0.90[ASN][1000 genomes]
rs4760690	0.90[ASN][1000 genomes]
rs4760695	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4760696	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4760697	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs58952582	0.85[AMR][1000 genomes]
rs60106007	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60761335	0.85[AMR][1000 genomes]
rs61343568	0.91[ASN][1000 genomes]
rs61918806	0.85[AMR][1000 genomes]
rs61918809	0.80[AMR][1000 genomes]
rs61918810	0.85[AMR][1000 genomes]
rs6580659	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7135779	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs719008	0.93[JPT][hapmap]
rs725454	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7299135	0.93[JPT][hapmap]
rs7299271	0.93[JPT][hapmap]
rs73102065	0.85[AMR][1000 genomes]
rs73102067	0.82[AMR][1000 genomes]
rs7485355	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7486424	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs886588	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs9634261	0.87[JPT][hapmap]
rs989144	1.00[JPT][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11168413	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11168413	RP1-228P16.1	cis	Thyroid	GTEx
rs11168413	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48501200-48512200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr12:48505200-48512000	Weak transcription	Hela-S3	cervix
3	chr12:48509200-48511600	Weak transcription	K562	blood

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