Variant report

Variant	rs2997190
Chromosome Location	chr13:37641876-37641877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1199951	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1199956	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199960	0.90[EUR][1000 genomes]
rs1199962	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1199963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199966	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1199972	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199974	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199977	0.90[EUR][1000 genomes]
rs1199978	0.90[EUR][1000 genomes]
rs1199979	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199980	0.90[EUR][1000 genomes]
rs1199981	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1199982	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1199983	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1199984	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1199987	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1199988	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199989	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12428936	0.81[EUR][1000 genomes]
rs12429860	0.83[EUR][1000 genomes]
rs1336755	0.98[EUR][1000 genomes]
rs1543738	1.00[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs1764481	0.90[EUR][1000 genomes]
rs1764483	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1764484	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1764486	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1764487	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1764488	0.91[EUR][1000 genomes]
rs1924418	0.94[EUR][1000 genomes]
rs1924422	0.90[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs1924426	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1937760	0.91[EUR][1000 genomes]
rs1937761	0.90[CEU][hapmap]
rs2093817	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2147169	0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes]
rs2181788	0.81[CEU][hapmap]
rs2211618	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2323165	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2323392	0.89[EUR][1000 genomes]
rs2669893	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2769543	0.89[CEU][hapmap]
rs2785620	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2801799	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2997183	1.00[ASW][hapmap]
rs2997189	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2997193	0.86[EUR][1000 genomes]
rs3858859	0.93[EUR][1000 genomes]
rs4291799	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs4941854	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes]
rs4941855	0.81[AMR][1000 genomes]
rs4941856	0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs4943441	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs4943442	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6563506	0.81[CEU][hapmap]
rs6563507	0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes]
rs6563508	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6563509	0.94[EUR][1000 genomes]
rs675108	0.82[CEU][hapmap]
rs73175079	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7317750	0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs7320899	0.94[EUR][1000 genomes]
rs7321129	0.90[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap]
rs7326688	0.98[EUR][1000 genomes]
rs7338929	0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs7339296	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7983986	0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs7989205	0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs7989380	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7991057	0.90[CEU][hapmap]
rs7995098	0.90[EUR][1000 genomes]
rs7997310	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs8001662	0.94[EUR][1000 genomes]
rs9532001	0.90[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap]
rs9532004	0.90[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs9532005	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes]
rs9547707	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs9547715	0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs9547717	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs9547718	0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs9547721	0.95[EUR][1000 genomes]
rs9547725	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9576154	0.90[CEU][hapmap]
rs9576162	0.98[EUR][1000 genomes]
rs9603121	0.90[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]

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
rs2997190	FAM48A	Cis_1M	lymphoblastoid	RTeQTL
rs2997190	SUPT20H	cis	Whole Blood	GTEx

Chromatin state (count:3 , 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
3	chr13:37641800-37642200	Enhancers	GM12878-XiMat	blood

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