Variant report

Variant	rs590286
Chromosome Location	chr1:146545604-146545605
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:146529795..146532554-chr1:146543290..146546177,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1596236	0.85[CEU][hapmap]
rs17160592	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2477568	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2477569	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2477570	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3011808	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3011809	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3011810	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4492676	0.82[EUR][1000 genomes]
rs4494193	0.81[EUR][1000 genomes]
rs4623760	0.81[EUR][1000 genomes]
rs492243	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs493000	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs494122	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4950302	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4950354	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4950355	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4950356	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs4950358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4950359	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4950360	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4950361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950362	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs517201	0.88[GIH][hapmap]
rs535827	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs551568	0.93[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs556976	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56060937	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs575115	0.86[CHB][hapmap]
rs584107	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59064267	0.82[EUR][1000 genomes]
rs604716	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs618575	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs618622	0.84[EUR][1000 genomes]
rs630630	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs632334	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs632861	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs647596	0.86[CHB][hapmap]
rs648937	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs659728	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs660096	0.84[EUR][1000 genomes]
rs660604	0.83[EUR][1000 genomes]
rs661116	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs675782	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs676288	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs678111	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs685741	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs719969	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs942689	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9659068	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9663073	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs976620	0.80[CEU][hapmap]
rs976621	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs976622	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
15	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
16	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
17	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs590286	CHD1L	cis	Whole Blood	GTEx
rs590286	CHD1L	cis	cerebellum	SCAN
rs590286	RP11-325P15.1	cis	lung	GTEx
rs590286	PRKAB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146545000-146547800	Weak transcription	Liver	Liver
2	chr1:146545400-146548200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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