Variant report

Variant	rs838517
Chromosome Location	chr1:119860286-119860287
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:119859568..119860444-chr1:119908558..119909246,2	K562	blood:
2	chr1:119857728..119859280-chr1:119859990..119862431,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WARS2-1	chr1:119860048-119860550	XLOC_000984
2	lnc-WARS2-2	chr1:119859984-119860550	NONHSAT005550

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10754394	0.93[EUR][1000 genomes]
rs10802089	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10923796	0.93[EUR][1000 genomes]
rs1409056	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418024	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1418025	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1891224	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2153738	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2226102	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2243981	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2253988	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2254528	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2254664	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2257016	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2265628	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2265630	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2477889	0.82[EUR][1000 genomes]
rs2477890	0.82[EUR][1000 genomes]
rs2885445	0.93[EUR][1000 genomes]
rs6428814	0.93[EUR][1000 genomes]
rs6672571	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs699771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838512	0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838513	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs838514	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs838515	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838516	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs838519	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs838520	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs838523	0.82[EUR][1000 genomes]
rs838524	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838525	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838526	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838527	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs866788	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs947422	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs947423	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs947424	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs947425	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv917091	chr1:119688975-120023222	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv547615	chr1:119828542-119875730	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
6	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	esv2761649	chr1:119840645-119925936	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119850800-119864600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:119858200-119862200	Weak transcription	Liver	Liver
3	chr1:119858800-119861200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:119859400-119869800	Weak transcription	Right Atrium	heart
5	chr1:119859800-119861000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:119860000-119860800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:119860000-119861600	Flanking Active TSS	GM12878-XiMat	blood
8	chr1:119860200-119861000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:119860200-119866400	Weak transcription	Fetal Thymus	thymus

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