Variant report

Variant	rs7538682
Chromosome Location	chr1:146610109-146610110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:146576066..146579009-chr1:146608253..146611072,2	K562	blood:
2	chr1:146608374..146610192-chr1:146634661..146636829,2	MCF-7	breast:
3	chr1:146553177..146556233-chr1:146608054..146610510,4	K562	blood:
4	chr1:146580378..146582055-chr1:146607503..146610346,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230832	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11809339	0.85[EUR][1000 genomes]
rs11811023	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12046706	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12144722	0.89[ASN][1000 genomes]
rs1372820	0.84[ASN][1000 genomes]
rs17159914	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17159924	0.84[EUR][1000 genomes]
rs17355398	0.87[EUR][1000 genomes]
rs17355419	0.86[EUR][1000 genomes]
rs17355474	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17355509	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17359629	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1813002	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1822304	0.93[ASN][1000 genomes]
rs1822309	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1932977	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2014106	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2077749	0.93[ASN][1000 genomes]
rs2083720	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28381210	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2883434	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766519	0.82[EUR][1000 genomes]
rs3766520	0.82[EUR][1000 genomes]
rs3766522	0.89[EUR][1000 genomes]
rs4558036	0.85[ASN][1000 genomes]
rs4950304	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4950305	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4950306	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4950308	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4950367	0.84[EUR][1000 genomes]
rs4950371	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4950373	0.81[EUR][1000 genomes]
rs4950379	0.86[EUR][1000 genomes]
rs4950382	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4950384	0.84[EUR][1000 genomes]
rs55697094	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55791847	0.87[EUR][1000 genomes]
rs55799799	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55828524	0.87[EUR][1000 genomes]
rs55963049	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56012243	0.82[EUR][1000 genomes]
rs56080828	0.83[EUR][1000 genomes]
rs56151278	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56198825	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56864370	0.80[EUR][1000 genomes]
rs61838936	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61838937	0.84[EUR][1000 genomes]
rs61838938	0.85[EUR][1000 genomes]
rs61838944	0.86[EUR][1000 genomes]
rs61838945	0.86[EUR][1000 genomes]
rs61838947	0.86[EUR][1000 genomes]
rs61838951	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6593745	0.87[ASN][1000 genomes]
rs6660507	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718369	0.90[ASN][1000 genomes]
rs720609	0.93[ASN][1000 genomes]
rs72706428	0.86[EUR][1000 genomes]
rs72706441	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72706444	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72708536	0.84[EUR][1000 genomes]
rs7514808	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7514970	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7515160	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7523021	0.87[ASN][1000 genomes]
rs7523975	0.84[EUR][1000 genomes]
rs7525703	0.93[ASN][1000 genomes]
rs7527894	0.87[ASN][1000 genomes]
rs7541393	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7548475	0.92[ASN][1000 genomes]
rs972368	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7538682	RP11-337C18.8	cis	Thyroid	GTEx
rs7538682	CHD1L	cis	Whole Blood	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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