Variant report

Variant	rs2462479
Chromosome Location	chr10:54793779-54793780
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	chr10:54793499..54796412-chr10:54801093..54803641,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10508984	0.91[EUR][1000 genomes]
rs10740531	0.90[EUR][1000 genomes]
rs10824852	0.80[CEU][hapmap];0.94[JPT][hapmap]
rs10824856	0.90[EUR][1000 genomes]
rs10824857	0.93[EUR][1000 genomes]
rs10824859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10824860	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11003335	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11003336	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11003339	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11003340	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11003341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11003343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812875	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11819148	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12360114	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1539513	0.80[CEU][hapmap];0.94[JPT][hapmap]
rs1917190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917194	0.90[EUR][1000 genomes]
rs1917195	0.90[EUR][1000 genomes]
rs1917196	0.90[EUR][1000 genomes]
rs1917197	0.91[EUR][1000 genomes]
rs1917205	0.89[EUR][1000 genomes]
rs1949813	0.90[EUR][1000 genomes]
rs1949814	0.91[EUR][1000 genomes]
rs2248319	0.89[EUR][1000 genomes]
rs2248678	0.89[EUR][1000 genomes]
rs2253152	0.91[EUR][1000 genomes]
rs2253266	0.91[EUR][1000 genomes]
rs2253468	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2264663	0.91[EUR][1000 genomes]
rs2265880	0.89[EUR][1000 genomes]
rs2492354	0.83[EUR][1000 genomes]
rs2891425	0.89[JPT][hapmap]
rs2891426	0.84[EUR][1000 genomes]
rs7069155	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7092980	0.80[CEU][hapmap];0.89[JPT][hapmap]
rs72800376	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72800377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895404	chr10:54545590-54850707	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043809	chr10:54645158-54860817	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv540627	chr10:54645158-54860817	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv467201	chr10:54697623-54929003	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv550906	chr10:54697623-54929003	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv470939	chr10:54700783-54917339	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv467202	chr10:54735164-54830687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv550907	chr10:54735164-54830687	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv895405	chr10:54765608-54824741	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv508585	chr10:54769376-54796804	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv895406	chr10:54780677-54830687	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1821304	chr10:54784919-54794208	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv1828095	chr10:54784919-54794208	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv1851757	chr10:54784919-54794208	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2462479	RP11-319F12.2	cis	Thyroid	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54790000-54793800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr10:54790800-54794200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr10:54791200-54798000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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