Variant report

Variant	rs957293
Chromosome Location	chr2:145833187-145833188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:145831836..145834513-chr2:145842893..145844887,2	K562	blood:
2	chr2:145831278..145834150-chr2:145834537..145836320,2	K562	blood:
3	chr2:145831278..145833894-chr2:145834820..145837755,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARHGAP15-6	chr2:145830091-145834291	NONHSAT074787
2	lnc-ARHGAP15-6	chr2:145830091-145834296	ENSG00000226674

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1006923	0.90[ASN][1000 genomes]
rs10206585	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10928241	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125128	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12474485	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476764	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12476923	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477111	0.90[ASN][1000 genomes]
rs12691704	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691705	0.84[AFR][1000 genomes]
rs12992411	0.90[ASN][1000 genomes]
rs12995180	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13015800	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028626	0.84[AFR][1000 genomes]
rs13384504	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389190	0.90[ASN][1000 genomes]
rs13428423	0.90[ASN][1000 genomes]
rs1819055	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1830318	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830319	0.82[AFR][1000 genomes]
rs1830320	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830321	0.84[AFR][1000 genomes]
rs1852684	0.84[AFR][1000 genomes]
rs1852686	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1881409	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881410	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252654	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2663966	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34029033	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34372836	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35462154	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35805189	0.95[ASN][1000 genomes]
rs6430076	0.90[ASN][1000 genomes]
rs6430078	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6721988	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725803	0.84[AFR][1000 genomes]
rs6747171	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747275	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749506	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7423637	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562803	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7604735	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7607110	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787427	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs957292	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002563	chr2:145182201-145863253	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv535957	chr2:145182201-145863253	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv932113	chr2:145515124-145844491	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv431768	chr2:145741527-145981491	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv875262	chr2:145830053-145888369	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv875263	chr2:145830053-145892427	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv875264	chr2:145830053-145911634	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs957293	PTPDC1	trans	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145827800-145833200	Weak transcription	A549	lung
2	chr2:145828600-145833400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:145830400-145863200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:145832800-145833400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:145832800-145833400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:145832800-145834400	Enhancers	Liver	Liver

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