Variant report

Variant	rs10247990
Chromosome Location	chr7:12201160-12201161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:12193169..12195612-chr7:12198878..12201480,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10214993	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10230634	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242473	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10242902	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10254924	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10257938	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12532313	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1369493	1.00[ASN][1000 genomes]
rs1435540	1.00[ASN][1000 genomes]
rs1595014	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16877301	0.83[EUR][1000 genomes]
rs17593950	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17664581	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17664676	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1990599	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991991	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2356058	0.95[ASN][1000 genomes]
rs2356059	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2356061	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28805088	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28807228	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34488298	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4721051	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55757340	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55953233	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58648544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6460888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6460889	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs714759	1.00[ASN][1000 genomes]
rs73057646	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73057649	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73059619	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73059629	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73059631	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73059637	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73059643	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7776528	1.00[ASN][1000 genomes]
rs7779920	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7795554	0.95[ASN][1000 genomes]
rs7799757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7799943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[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	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv887614	chr7:11778424-12211198	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1023608	chr7:12064114-12247520	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1021710	chr7:12164993-12251790	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv887627	chr7:12178793-12227892	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv887628	chr7:12186502-12227892	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10247990	PHF14	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12198600-12201600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr7:12198600-12208200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:12199000-12201200	Weak transcription	A549	lung
4	chr7:12200800-12201200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:12201000-12202200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:12201000-12202600	Enhancers	NH-A	brain
7	chr7:12201000-12202800	Enhancers	Hela-S3	cervix

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