Variant report

Variant	rs3822939
Chromosome Location	chr6:133849789-133849790
allele	A/G
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:17)

rs_ID	r²[population]
rs10872407	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs212765	0.84[CEU][hapmap]
rs212766	0.84[CEU][hapmap]
rs212773	0.84[CEU][hapmap]
rs212774	0.84[CEU][hapmap]
rs212775	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs212776	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs212777	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277083	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2327352	0.82[AFR][1000 genomes]
rs478907	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs561826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs598699	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6899927	0.82[JPT][hapmap]
rs6913726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9385650	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9483586	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[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	nsv886681	chr6:133833284-133869617	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3822939	VNN3	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133823200-133869600	Weak transcription	Psoas Muscle	Psoas
2	chr6:133824200-133854200	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:133824400-133854800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:133824400-133861600	Weak transcription	Ovary	ovary
5	chr6:133825600-133857200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:133826600-133862400	Weak transcription	Fetal Lung	lung
7	chr6:133836800-133854000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:133837400-133863600	Weak transcription	A549	lung
9	chr6:133845400-133856400	Weak transcription	Fetal Kidney	kidney
10	chr6:133845400-133860400	Weak transcription	HSMMtube	muscle
11	chr6:133847400-133854000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:133847800-133853800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:133847800-133856400	Weak transcription	Hela-S3	cervix
14	chr6:133849600-133850000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:133849600-133850000	Enhancers	Right Atrium	heart

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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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