Variant report

Variant	rs7542951
Chromosome Location	chr1:146812058-146812059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 141 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10736837	0.82[AMR][1000 genomes]
rs10751409	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs10751410	0.82[AMR][1000 genomes]
rs10793657	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs10793658	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs10793661	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs10900332	1.00[JPT][hapmap]
rs10900333	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs10900336	0.82[AMR][1000 genomes]
rs11239954	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs11239970	0.81[AMR][1000 genomes]
rs11239971	0.82[AMR][1000 genomes]
rs11800580	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs12046626	1.00[JPT][hapmap]
rs17159914	0.90[CEU][hapmap]
rs17159924	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs17160050	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs17160051	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs17356184	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs17356219	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs17356233	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs17356240	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs17356492	0.88[AMR][1000 genomes]
rs17356735	1.00[CHB][hapmap]
rs17360443	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs1932977	0.84[CEU][hapmap]
rs1932980	0.81[AMR][1000 genomes]
rs1932981	0.82[AMR][1000 genomes]
rs1999820	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2210954	0.82[AMR][1000 genomes]
rs2354428	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs2883323	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs2883324	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs3737849	0.81[AMR][1000 genomes]
rs3737850	0.81[AMR][1000 genomes]
rs3737853	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs3737854	0.82[AMR][1000 genomes]
rs3737855	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs3766519	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs3766520	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs3766522	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs4264042	0.82[AMR][1000 genomes]
rs4284292	0.82[AMR][1000 genomes]
rs4301678	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs4326679	0.82[AMR][1000 genomes]
rs4373796	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs4385773	0.82[AMR][1000 genomes]
rs4453096	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs4518968	0.82[AMR][1000 genomes]
rs4568882	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs4950315	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs4950316	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs4950318	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs4950319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs4950382	0.90[CEU][hapmap]
rs4950392	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs4950409	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4950415	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6537	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs6593756	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs6593758	0.82[AMR][1000 genomes]
rs6593760	0.82[AMR][1000 genomes]
rs6593762	0.81[AMR][1000 genomes]
rs6593763	0.82[AMR][1000 genomes]
rs6593764	0.82[AMR][1000 genomes]
rs6593765	0.82[AMR][1000 genomes]
rs6593767	0.82[AMR][1000 genomes]
rs6659630	0.82[AMR][1000 genomes]
rs6660985	0.82[AMR][1000 genomes]
rs6665597	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs6674987	0.82[AMR][1000 genomes]
rs6677762	0.82[AMR][1000 genomes]
rs6692355	0.82[AMR][1000 genomes]
rs6692453	0.82[AMR][1000 genomes]
rs6697022	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs6703892	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs72691041	0.83[AMR][1000 genomes]
rs72691054	0.90[AMR][1000 genomes]
rs72691090	0.88[AMR][1000 genomes]
rs72691093	0.88[AMR][1000 genomes]
rs72691095	0.90[AMR][1000 genomes]
rs72691097	0.90[AMR][1000 genomes]
rs72691098	0.90[AMR][1000 genomes]
rs72691102	0.90[AMR][1000 genomes]
rs72692904	0.90[AMR][1000 genomes]
rs72692905	0.90[AMR][1000 genomes]
rs72692907	0.90[AMR][1000 genomes]
rs72692914	0.90[AMR][1000 genomes]
rs72692917	0.90[AMR][1000 genomes]
rs72692942	0.84[AMR][1000 genomes]
rs72692963	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72692965	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72692968	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72692971	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72692973	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72692975	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72692979	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs72692980	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs72694703	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7517324	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7519022	0.82[AMR][1000 genomes]
rs7526996	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7528700	0.82[AMR][1000 genomes]
rs7544598	0.81[AMR][1000 genomes]
rs7554833	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs7555817	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS 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	93 gene(s)	inside rSNPs	diseases
14	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
15	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
16	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	49 gene(s)	inside rSNPs	diseases
17	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
18	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv437047	chr1:146643555-146841602	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
20	nsv1005809	chr1:146647822-146886419	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv535134	chr1:146647822-146886419	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
23	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
24	nsv547676	chr1:146686228-146996047	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
25	nsv872260	chr1:146767353-146826675	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv872261	chr1:146767353-146842342	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
27	nsv872262	chr1:146767353-146901677	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
28	nsv1001520	chr1:146774986-146848201	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv1003769	chr1:146774986-146886419	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
30	nsv998093	chr1:146779395-146913979	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
31	esv3395217	chr1:146784718-146932376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
32	nsv872263	chr1:146785157-146923557	Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
33	nsv872264	chr1:146791729-146923557	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
34	nsv946305	chr1:146805697-146829259	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
35	nsv534063	chr1:146807433-147381411	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7542951	CHD1L	cis	Whole Blood	GTEx
rs7542951	CHD1L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146809200-146814000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:146810000-146812800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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