Variant report

Variant	rs12488219
Chromosome Location	chr3:42384778-42384779
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42380106..42383647-chr3:42383812..42387475,4	K562	blood:

Variant related genes	Relation type
ENSG00000229572	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1015296	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1015297	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12489819	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12498026	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12636595	0.81[AMR][1000 genomes]
rs13061663	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13063762	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13063772	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13063871	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13070178	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13073794	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13076131	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13077160	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13077349	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13080086	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13081316	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13084389	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13084687	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13086635	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13093997	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13095022	0.85[EUR][1000 genomes]
rs13098757	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13098758	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13099012	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1442268	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17030429	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17074119	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1837907	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1837908	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2240862	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2240863	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs33910510	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35547241	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55642108	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55819908	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56200813	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56267682	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56345349	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56351527	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62257781	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442135	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6442136	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6442137	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6763701	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6765610	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6772380	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6772637	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6775205	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6775430	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6778018	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6781346	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6786175	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6786895	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6799449	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6799660	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6799966	0.91[AMR][1000 genomes];0.94[EUR][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	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1009125	chr3:41953873-42472253	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
3	nsv536549	chr3:41953873-42472253	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34472	chr3:42314655-42391480	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2756986	chr3:42360106-42403380	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
7	esv2759144	chr3:42360106-42403380	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv1008543	chr3:42372639-42401033	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42384000-42387000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:42384200-42385800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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