Variant report

Variant	rs580852
Chromosome Location	chr1:146523045-146523046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10157212	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10900384	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs11240094	0.89[CHB][hapmap]
rs11811023	0.88[JPT][hapmap]
rs12070797	0.85[ASN][1000 genomes]
rs12122453	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs12122534	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs12125491	0.82[ASN][1000 genomes]
rs12141387	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs1596236	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17159924	0.88[JPT][hapmap]
rs17160592	0.89[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17355398	0.88[JPT][hapmap]
rs17355509	0.88[JPT][hapmap]
rs17359629	0.88[JPT][hapmap]
rs1867140	0.85[ASN][1000 genomes]
rs1925343	0.90[CHB][hapmap]
rs2031481	0.90[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs2477567	0.82[ASN][1000 genomes]
rs2477568	0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2477569	0.89[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2477570	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2584952	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2985722	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3011803	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011808	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3011809	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3011810	0.85[ASN][1000 genomes]
rs3766519	0.88[JPT][hapmap]
rs3766520	0.88[JPT][hapmap]
rs3766522	0.88[JPT][hapmap]
rs4492676	0.81[ASN][1000 genomes]
rs4494193	0.84[ASN][1000 genomes]
rs4623760	0.83[ASN][1000 genomes]
rs483181	0.85[ASN][1000 genomes]
rs492243	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs493000	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs494122	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4950301	0.85[ASN][1000 genomes]
rs4950302	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4950303	0.85[ASN][1000 genomes]
rs4950304	0.88[JPT][hapmap]
rs4950306	0.88[JPT][hapmap]
rs4950308	0.88[JPT][hapmap]
rs4950332	0.88[JPT][hapmap]
rs4950354	0.89[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4950355	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4950356	0.90[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs4950359	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4950360	0.85[ASN][1000 genomes]
rs4950361	0.83[GIH][hapmap]
rs4950362	0.85[ASN][1000 genomes]
rs4950364	0.85[ASN][1000 genomes]
rs4950371	0.88[JPT][hapmap]
rs499605	0.82[ASN][1000 genomes]
rs517201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524016	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs527874	0.82[ASN][1000 genomes]
rs527976	0.82[ASN][1000 genomes]
rs535827	0.89[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs540969	0.85[ASN][1000 genomes]
rs556976	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56060937	0.85[ASN][1000 genomes]
rs56359955	0.83[ASN][1000 genomes]
rs576743	0.83[ASN][1000 genomes]
rs584107	0.89[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58670838	0.85[ASN][1000 genomes]
rs59064267	0.85[ASN][1000 genomes]
rs604106	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604716	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs612971	0.85[ASN][1000 genomes]
rs614763	0.81[CHB][hapmap];0.80[CHD][hapmap];0.83[ASN][1000 genomes]
rs618575	0.85[ASN][1000 genomes]
rs618622	0.83[ASN][1000 genomes]
rs630630	0.90[ASN][1000 genomes]
rs632334	0.85[ASN][1000 genomes]
rs632861	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs648937	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6593732	1.00[JPT][hapmap]
rs659728	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs660096	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs660604	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs661116	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6686480	0.88[JPT][hapmap]
rs671690	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675782	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs675809	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs676288	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs678111	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs685741	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs719969	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs72704299	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72706414	0.85[ASN][1000 genomes]
rs72706418	0.84[ASN][1000 genomes]
rs7515160	0.88[JPT][hapmap]
rs7541393	0.88[JPT][hapmap]
rs942689	0.89[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9659068	0.85[ASN][1000 genomes]
rs9663073	0.88[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs972368	0.88[JPT][hapmap]
rs976620	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs976621	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs976622	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428224	chr1:145613243-146553918	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv2757753	chr1:145883119-146697542	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
5	nsv872253	chr1:146494246-146548549	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv872254	chr1:146503841-146544721	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
8	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer 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	110 gene(s)	inside rSNPs	diseases
9	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
11	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
12	nsv946298	chr1:146510432-146557539	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
13	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs580852	CHD1L	cis	cerebellum	SCAN
rs580852	RP11-325P15.1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146520000-146523800	Weak transcription	GM12878-XiMat	blood
2	chr1:146521400-146523600	Weak transcription	Primary B cells from cord blood	blood
3	chr1:146521600-146527800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:146521800-146523600	Weak transcription	Primary B cells from peripheral blood	blood

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