Variant report

Variant	rs3799280
Chromosome Location	chr6:73888451-73888452
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]
rs1970547	0.84[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1970549	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs2027545	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2350385	0.95[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2350386	0.84[MEX][hapmap]
rs2882404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882405	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6907229	0.83[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs6937240	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6937253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756501	0.84[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9343015	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9351979	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9351980	0.83[EUR][1000 genomes]
rs9446861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1022151	chr6:73876795-73996828	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv538304	chr6:73876795-73996828	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3799280	EEF1A1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73867600-73890400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:73867600-73890400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:73869000-73904200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:73876800-73889800	Weak transcription	HSMM	muscle
5	chr6:73878400-73890200	Weak transcription	Psoas Muscle	Psoas
6	chr6:73879800-73890000	Weak transcription	HMEC	breast
7	chr6:73880200-73889600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:73884800-73889400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:73884800-73903600	Weak transcription	Primary T cells from cord blood	blood
10	chr6:73887000-73890200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:73887600-73890000	Weak transcription	GM12878-XiMat	blood
12	chr6:73887600-73903600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:73887800-73890200	Weak transcription	Primary B cells from peripheral blood	blood

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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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