Variant report

Variant	rs7549150
Chromosome Location	chr1:221661342-221661343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10158337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10159173	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13373986	0.83[EUR][1000 genomes]
rs13375835	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1599086	0.83[EUR][1000 genomes]
rs17010091	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17010163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17010165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61553069	0.83[EUR][1000 genomes]
rs6699367	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs74146104	0.83[EUR][1000 genomes]
rs9660276	0.83[EUR][1000 genomes]
rs9724647	0.83[EUR][1000 genomes]
rs9724682	0.83[EUR][1000 genomes]
rs9727723	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873200	chr1:221644180-221843191	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7549150	PHYH	trans	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221652200-221669000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:221659800-221662800	Enhancers	Hela-S3	cervix
3	chr1:221660400-221662800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:221661000-221661600	Enhancers	NHEK	skin
5	chr1:221661000-221661800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:221661000-221661800	Enhancers	HSMMtube	muscle
7	chr1:221661000-221662000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:221661000-221662000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:221661000-221662000	Enhancers	Stomach Mucosa	stomach
10	chr1:221661000-221662000	Enhancers	HSMM	muscle
11	chr1:221661000-221662000	Enhancers	Osteobl	bone
12	chr1:221661000-221662200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:221661000-221662400	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr1:221661200-221661600	Flanking Active TSS	A549	lung
15	chr1:221661200-221661800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:221661200-221662000	Enhancers	NHLF	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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