Variant report

Variant	rs9977974
Chromosome Location	chr21:28477949-28477950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1041423	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1041424	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10482980	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17600993	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17659214	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17660338	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1788311	1.00[CHD][hapmap];1.00[MKK][hapmap]
rs233588	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2830664	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2830676	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2830685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2830690	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2830699	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28463781	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28549866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs404112	1.00[AMR][1000 genomes]
rs7279282	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73187872	0.88[AMR][1000 genomes]
rs73187879	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73187887	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73187889	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73187890	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73187892	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73187893	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73187894	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73187895	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73187898	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73189810	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73189877	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9284446	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9975373	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9976558	0.94[AMR][1000 genomes]
rs9984557	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2758532	chr21:28380230-28540443	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	esv2758817	chr21:28380230-28540443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	nsv1062808	chr21:28443252-28537209	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
5	nsv544414	chr21:28443252-28537209	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9977974	FRMD4A	trans	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28477000-28478000	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr21:28477000-28478200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr21:28477200-28478000	Enhancers	HSMMtube	muscle
4	chr21:28477200-28478200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr21:28477200-28478200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr21:28477200-28478200	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr21:28477200-28478200	Enhancers	NHDF-Ad	bronchial
8	chr21:28477200-28478400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr21:28477200-28478400	Enhancers	Adipose Nuclei	Adipose
10	chr21:28477200-28479400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr21:28477400-28478000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr21:28477400-28478000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr21:28477400-28478200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr21:28477400-28478200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr21:28477400-28478200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr21:28477400-28478200	Enhancers	Ovary	ovary
17	chr21:28477600-28478000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr21:28477600-28478000	Enhancers	NHEK	skin
19	chr21:28477600-28478800	Enhancers	Fetal Kidney	kidney
20	chr21:28477600-28479000	Enhancers	Osteobl	bone
21	chr21:28477800-28478000	Enhancers	Hela-S3	cervix

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