Variant report

Variant	rs3807412
Chromosome Location	chr7:38537256-38537257
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10248732	0.98[LWK][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes]
rs10249106	0.98[LWK][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes]
rs10253139	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10274194	0.88[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10277748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1030017	0.82[EUR][1000 genomes]
rs2028210	1.00[ASW][hapmap];0.81[GIH][hapmap];0.98[LWK][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes]
rs2043786	0.88[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2299946	0.83[JPT][hapmap]
rs3778878	0.98[LWK][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes]
rs3807415	0.89[EUR][1000 genomes]
rs4720279	0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs4720280	0.95[JPT][hapmap];0.83[TSI][hapmap]
rs4720285	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4720287	0.88[ASW][hapmap];0.98[LWK][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes]
rs6951641	0.92[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs722334	0.85[CEU][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7778991	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7801792	0.81[EUR][1000 genomes]
rs7811148	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs887967	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs967025	0.82[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3807412	LOC648852	N/A	lymphoblastoid	RTeQTL
rs3807412	EEPD1	cis	parietal	SCAN
rs3807412	TRGV5	cis	Whole Blood	GTEx
rs3807412	TARP	cis	cerebellum	SCAN
rs3807412	TRGV5	Cis_1M	lymphoblastoid	RTeQTL
rs3807412	VPS41	cis	cerebellum	SCAN

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	chr7:38524000-38543400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:38524200-38545000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:38528600-38553000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:38531400-38544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:38531800-38543800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr7:38532000-38540200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:38533200-38542800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr7:38534200-38542400	Weak transcription	Aorta	Aorta

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