Variant report

Variant	rs1199988
Chromosome Location	chr13:37642703-37642704
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	chr13:37631468..37633109-chr13:37642109..37643855,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1199951	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199956	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1199960	0.88[EUR][1000 genomes]
rs1199962	0.90[EUR][1000 genomes]
rs1199963	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199966	0.86[EUR][1000 genomes]
rs1199972	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1199974	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1199977	0.91[EUR][1000 genomes]
rs1199978	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1199979	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1199980	0.91[EUR][1000 genomes]
rs1199981	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199982	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199983	0.86[EUR][1000 genomes]
rs1199984	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199986	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199987	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12429860	0.82[EUR][1000 genomes]
rs1336755	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1543738	0.94[EUR][1000 genomes]
rs1764481	0.88[EUR][1000 genomes]
rs1764483	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1764484	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1764486	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1764487	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1764488	0.90[EUR][1000 genomes]
rs1924418	0.95[EUR][1000 genomes]
rs1924426	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1937760	0.90[EUR][1000 genomes]
rs2093817	0.95[EUR][1000 genomes]
rs2211618	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2323392	0.90[EUR][1000 genomes]
rs2669893	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2785620	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2801799	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2997189	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2997190	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2997193	0.85[EUR][1000 genomes]
rs3858859	0.94[EUR][1000 genomes]
rs4943442	0.80[EUR][1000 genomes]
rs6563508	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6563509	0.95[EUR][1000 genomes]
rs73175079	0.88[EUR][1000 genomes]
rs7320899	0.95[EUR][1000 genomes]
rs7326688	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7339296	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7989380	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7995098	0.88[EUR][1000 genomes]
rs7997310	0.95[EUR][1000 genomes]
rs8001662	0.95[EUR][1000 genomes]
rs9547721	0.97[EUR][1000 genomes]
rs9547725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9576162	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3377840	chr13:37631001-37656330	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1199988	SUPT20H	cis	Whole Blood	GTEx
rs1199988	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37634600-37643800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:37640800-37644800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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