Variant report

Variant	rs3807411
Chromosome Location	chr7:38546848-38546849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10274615	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10499602	0.90[EUR][1000 genomes]
rs11763360	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1561309	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs17410710	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1982179	0.91[EUR][1000 genomes]
rs2196673	0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3807404	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823592	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57760385	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62444214	0.91[EUR][1000 genomes]
rs62444215	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62444216	0.90[EUR][1000 genomes]
rs62444217	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3807411	TRGV5	cis	Whole Blood	GTEx
rs3807411	TRGV4	cis	Whole Blood	GTEx
rs3807411	LOC648852	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38502600-38549400	Weak transcription	Fetal Stomach	stomach
2	chr7:38528600-38553000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:38545600-38547000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:38545800-38547200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr7:38546000-38547600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:38546200-38547400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:38546400-38548000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:38546600-38547000	Enhancers	NHDF-Ad	bronchial
9	chr7:38546600-38547400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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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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