Variant report

Variant	rs12088549
Chromosome Location	chr1:92707504-92707505
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	chr1:92706202..92709030-chr1:92713250..92715808,3	K562	blood:

Variant related genes	Relation type
ENSG00000174842	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10399670	1.00[EUR][1000 genomes]
rs10399724	1.00[EUR][1000 genomes]
rs10399865	1.00[EUR][1000 genomes]
rs10399960	1.00[EUR][1000 genomes]
rs11164364	1.00[EUR][1000 genomes]
rs11166022	1.00[EUR][1000 genomes]
rs11166028	1.00[EUR][1000 genomes]
rs11166030	1.00[EUR][1000 genomes]
rs11166044	1.00[EUR][1000 genomes]
rs11166045	1.00[EUR][1000 genomes]
rs11166066	1.00[EUR][1000 genomes]
rs11166068	1.00[EUR][1000 genomes]
rs11166107	1.00[EUR][1000 genomes]
rs11166118	1.00[EUR][1000 genomes]
rs11166189	1.00[EUR][1000 genomes]
rs11166200	1.00[EUR][1000 genomes]
rs11166203	1.00[EUR][1000 genomes]
rs11166390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11166543	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12057625	1.00[EUR][1000 genomes]
rs12057715	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12057860	1.00[EUR][1000 genomes]
rs12058147	1.00[EUR][1000 genomes]
rs12059439	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12059473	1.00[EUR][1000 genomes]
rs12059645	1.00[EUR][1000 genomes]
rs12061480	1.00[EUR][1000 genomes]
rs12061953	1.00[EUR][1000 genomes]
rs12062143	1.00[EUR][1000 genomes]
rs12063053	1.00[EUR][1000 genomes]
rs12063404	1.00[EUR][1000 genomes]
rs12064015	1.00[EUR][1000 genomes]
rs12064732	1.00[EUR][1000 genomes]
rs12065163	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12065626	1.00[EUR][1000 genomes]
rs12065694	1.00[EUR][1000 genomes]
rs12065702	1.00[EUR][1000 genomes]
rs12066980	1.00[EUR][1000 genomes]
rs12067302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12068883	1.00[EUR][1000 genomes]
rs12069690	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12069984	1.00[EUR][1000 genomes]
rs12070249	1.00[EUR][1000 genomes]
rs12071033	1.00[EUR][1000 genomes]
rs12071088	1.00[EUR][1000 genomes]
rs12072804	1.00[EUR][1000 genomes]
rs12073274	1.00[EUR][1000 genomes]
rs12074384	1.00[EUR][1000 genomes]
rs12076399	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12076954	1.00[EUR][1000 genomes]
rs12078738	1.00[EUR][1000 genomes]
rs12080119	1.00[EUR][1000 genomes]
rs12080525	1.00[EUR][1000 genomes]
rs12085789	1.00[EUR][1000 genomes]
rs12086354	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12086426	1.00[EUR][1000 genomes]
rs12087282	1.00[EUR][1000 genomes]
rs12088142	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088562	1.00[EUR][1000 genomes]
rs12089666	1.00[EUR][1000 genomes]
rs12090217	1.00[EUR][1000 genomes]
rs12091427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12092747	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093038	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093590	1.00[EUR][1000 genomes]
rs12093905	1.00[EUR][1000 genomes]
rs12095429	1.00[EUR][1000 genomes]
rs12096979	1.00[EUR][1000 genomes]
rs12097184	1.00[EUR][1000 genomes]
rs1483020	1.00[EUR][1000 genomes]
rs1483021	1.00[EUR][1000 genomes]
rs1487538	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17100275	1.00[EUR][1000 genomes]
rs17131601	1.00[EUR][1000 genomes]
rs17131604	1.00[EUR][1000 genomes]
rs17131606	1.00[EUR][1000 genomes]
rs17131614	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17131625	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17131626	1.00[EUR][1000 genomes]
rs17131634	1.00[EUR][1000 genomes]
rs2046297	1.00[EUR][1000 genomes]
rs2170644	1.00[EUR][1000 genomes]
rs35166258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35428675	1.00[EUR][1000 genomes]
rs41344152	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs57820459	1.00[EUR][1000 genomes]
rs58471288	1.00[EUR][1000 genomes]
rs59366523	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59385116	1.00[EUR][1000 genomes]
rs59800659	1.00[EUR][1000 genomes]
rs60332284	1.00[EUR][1000 genomes]
rs6657876	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6679077	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72956818	1.00[EUR][1000 genomes]
rs72956832	1.00[EUR][1000 genomes]
rs72956833	1.00[EUR][1000 genomes]
rs72956863	1.00[EUR][1000 genomes]
rs72956874	1.00[EUR][1000 genomes]
rs72956893	1.00[EUR][1000 genomes]
rs72958705	1.00[AMR][1000 genomes]
rs72958718	1.00[AMR][1000 genomes]
rs72958765	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958768	1.00[EUR][1000 genomes]
rs72958786	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958791	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960813	1.00[EUR][1000 genomes]
rs72960817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960880	1.00[EUR][1000 genomes]
rs72960900	1.00[EUR][1000 genomes]
rs72962603	1.00[EUR][1000 genomes]
rs72962608	1.00[EUR][1000 genomes]
rs72962610	1.00[EUR][1000 genomes]
rs72962621	1.00[EUR][1000 genomes]
rs72962625	1.00[EUR][1000 genomes]
rs72962628	1.00[EUR][1000 genomes]
rs7512045	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7552286	1.00[EUR][1000 genomes]
rs9660398	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92705600-92726800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:92705800-92711400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:92705800-92729200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:92707200-92764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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