Variant report

Variant	rs3094138
Chromosome Location	chr6:30199016-30199017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1063280	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094079	0.86[AFR][1000 genomes]
rs3094137	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130385	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130390	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4476873	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959045	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261541	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261542	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261547	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261558	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9261588	0.86[AFR][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	nsv884058	chr6:30182395-30202429	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv884059	chr6:30190484-30199016	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv884060	chr6:30190640-30203602	Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3094138	FLJ35429	cis	multi-tissue	Pritchard
rs3094138	HLA-A	cis	multi-tissue	Pritchard
rs3094138	HCG22	cis	lymphoblastoid	seeQTL
rs3094138	PRSS16	cis	parietal	SCAN
rs3094138	HLA-H	cis	multi-tissue	Pritchard
rs3094138	HLA-F	cis	multi-tissue	Pritchard
rs3094138	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30197800-30200000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:30198000-30199200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:30198000-30199600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:30198200-30199800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:30198400-30199800	Enhancers	HSMMtube	muscle
6	chr6:30198800-30199400	Enhancers	HSMM	muscle

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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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