Variant report

Variant	rs1343041
Chromosome Location	chr10:54665442-54665443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10740527	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10762900	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10762901	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10824830	0.86[ASN][1000 genomes]
rs10824832	0.84[CHB][hapmap];0.94[ASN][1000 genomes]
rs10824833	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11003249	0.86[ASN][1000 genomes]
rs12241552	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs12415434	0.90[ASN][1000 genomes]
rs12416670	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1318675	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1343042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343061	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16935229	0.83[ASN][1000 genomes]
rs16935242	0.89[ASN][1000 genomes]
rs58685633	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7071994	0.80[ASN][1000 genomes]
rs7078097	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7083678	0.86[ASN][1000 genomes]
rs73345229	0.82[ASN][1000 genomes]
rs7910935	0.86[ASN][1000 genomes]
rs959332	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	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
3	nsv831877	chr10:54565135-54764638	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv467200	chr10:54585401-54726056	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv550905	chr10:54585401-54726056	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1041940	chr10:54621342-54737528	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	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
8	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

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54663400-54667600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:54664000-54667800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr10:54664000-54667800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:54664200-54667600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:54664200-54667600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr10:54664400-54668000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr10:54664600-54667600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:54664600-54668200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr10:54664800-54667600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr10:54665400-54665600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:54665400-54666400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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