Variant report

Variant	rs6582709
Chromosome Location	chr12:47817901-47817902
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10785684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10881116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11183971	0.82[JPT][hapmap]
rs11832323	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12314864	0.83[CHB][hapmap]
rs12581930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1919729	0.82[ASN][1000 genomes]
rs2015389	0.86[ASN][1000 genomes]
rs2097726	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2106837	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2188940	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2188943	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56140320	0.81[ASN][1000 genomes]
rs6582710	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582711	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6582713	0.80[ASN][1000 genomes]
rs721370	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs721371	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7295199	0.81[ASN][1000 genomes]
rs7312534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7979332	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs982648	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6582709	SLC38A4	cis	parietal	SCAN
rs6582709	RAPGEF3	cis	parietal	SCAN
rs6582709	RPAP3	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47802200-47820000	Weak transcription	Aorta	Aorta
2	chr12:47808000-47818800	Weak transcription	Hela-S3	cervix
3	chr12:47815200-47818600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:47816200-47820000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:47816800-47818200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:47817400-47819400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr12:47817800-47818600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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