Variant report

Variant	rs2059541
Chromosome Location	chr11:25316492-25316493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10834637	0.81[EUR][1000 genomes]
rs10834640	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10834641	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10834643	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11028562	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11028569	1.00[ASN][1000 genomes]
rs11028571	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11028588	0.81[ASN][1000 genomes]
rs12225365	0.91[ASN][1000 genomes]
rs12225694	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12793930	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12806211	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12806578	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17307806	0.81[ASN][1000 genomes]
rs1863367	0.97[ASN][1000 genomes]
rs2059543	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2114075	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2114076	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2404049	0.97[ASN][1000 genomes]
rs4922709	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4923261	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7949173	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7949239	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv553827	chr11:24858636-25379281	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2422339	chr11:25004617-25546665	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2757430	chr11:25088712-25322598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2759810	chr11:25088712-25365520	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1041326	chr11:25140415-25533851	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1049709	chr11:25150091-25605844	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv553859	chr11:25169641-25325799	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv467763	chr11:25172085-25600742	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv553860	chr11:25172085-25600742	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1050819	chr11:25175511-25592569	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv540970	chr11:25175511-25592569	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv2760599	chr11:25186984-26159450	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv2758258	chr11:25191953-25365520	Enhancers ZNF genes & repeats Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1043467	chr11:25210613-25691086	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv540971	chr11:25210613-25691086	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv897124	chr11:25230780-25364232	ZNF genes & repeats Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv553863	chr11:25244001-25332979	Enhancers ZNF genes & repeats Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv553864	chr11:25244001-25433466	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv897126	chr11:25277449-25362206	Enhancers ZNF genes & repeats Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
20	nsv897127	chr11:25293414-25386809	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv553865	chr11:25294118-25358529	Active TSS Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
22	nsv553866	chr11:25294118-25362206	Active TSS Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
23	nsv897128	chr11:25294229-25656452	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv1038851	chr11:25309135-25420610	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2059541	NELL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:25313800-25322800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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