Variant report

Variant	rs12429860
Chromosome Location	chr13:37713595-37713596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1199951	0.83[EUR][1000 genomes]
rs1199956	0.82[EUR][1000 genomes]
rs1199962	0.90[CEU][hapmap]
rs1199963	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs1199972	0.80[EUR][1000 genomes]
rs1199974	0.90[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs1199975	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1199979	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1199981	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs1199982	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs1199983	0.90[CEU][hapmap]
rs1199984	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs1199986	0.83[EUR][1000 genomes]
rs1199987	0.83[EUR][1000 genomes]
rs1199988	0.82[EUR][1000 genomes]
rs1199989	0.82[EUR][1000 genomes]
rs12428936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1336755	0.82[EUR][1000 genomes]
rs1543738	0.90[CEU][hapmap]
rs1764483	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs1764484	0.86[EUR][1000 genomes]
rs1764486	0.83[EUR][1000 genomes]
rs1764487	0.82[EUR][1000 genomes]
rs1764488	0.81[EUR][1000 genomes]
rs1924418	0.80[EUR][1000 genomes]
rs1924422	0.81[CEU][hapmap]
rs1924426	0.82[EUR][1000 genomes]
rs1937760	0.81[EUR][1000 genomes]
rs1937761	0.81[CEU][hapmap]
rs2093817	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs2147169	0.81[CEU][hapmap]
rs2211618	0.82[EUR][1000 genomes]
rs2323165	0.81[CEU][hapmap]
rs2669893	0.82[EUR][1000 genomes]
rs2785620	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs2997189	0.86[EUR][1000 genomes]
rs2997190	0.83[EUR][1000 genomes]
rs4291799	0.81[CEU][hapmap]
rs4941854	0.81[CEU][hapmap]
rs4941856	0.81[CEU][hapmap]
rs4943441	0.90[CEU][hapmap]
rs4943442	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6420362	1.00[YRI][hapmap]
rs6563507	0.81[CEU][hapmap]
rs6563508	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs6563509	0.80[EUR][1000 genomes]
rs73177067	0.86[AFR][1000 genomes]
rs73177070	0.86[AFR][1000 genomes]
rs7317750	0.81[CEU][hapmap]
rs7320899	0.80[EUR][1000 genomes]
rs7321129	0.81[CEU][hapmap]
rs7326688	0.82[EUR][1000 genomes]
rs7338929	0.81[CEU][hapmap]
rs7339296	0.82[EUR][1000 genomes]
rs7983986	0.81[CEU][hapmap]
rs7989205	0.81[CEU][hapmap]
rs7989380	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs7991057	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs7997310	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs8001662	0.80[EUR][1000 genomes]
rs9315459	1.00[YRI][hapmap]
rs9532001	0.81[CEU][hapmap]
rs9532004	0.81[CEU][hapmap]
rs9532005	0.81[CEU][hapmap]
rs9547707	0.81[CEU][hapmap]
rs9547715	0.81[CEU][hapmap]
rs9547718	0.81[CEU][hapmap]
rs9547725	0.81[EUR][1000 genomes]
rs9576154	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs9576162	0.82[EUR][1000 genomes]
rs9603121	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12429860	SUPT20H	cis	Whole Blood	GTEx
rs12429860	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37708200-37714200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr13:37708400-37714400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr13:37709200-37718200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr13:37710000-37714000	Enhancers	NHDF-Ad	bronchial
5	chr13:37710800-37718000	Weak transcription	NH-A	brain
6	chr13:37711400-37714200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr13:37711800-37713800	Enhancers	Osteobl	bone
8	chr13:37712600-37713600	Weak transcription	Adipose Nuclei	Adipose
9	chr13:37712600-37718200	Weak transcription	Hela-S3	cervix
10	chr13:37713400-37713800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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