Variant report

Variant	rs402020
Chromosome Location	chr6:133609328-133609329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11753937	0.83[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap]
rs12523816	0.83[CEU][hapmap]
rs211434	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs375189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377962	0.86[GIH][hapmap];0.81[MEX][hapmap]
rs385859	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs407038	0.89[ASN][1000 genomes]
rs4493757	0.86[ASN][1000 genomes]
rs519332	0.82[CEU][hapmap];0.93[MEX][hapmap]
rs572004	0.93[MEX][hapmap]
rs6569876	0.81[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs954917	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758080	chr6:133444719-133627364	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2759470	chr6:133444719-133627364	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv886678	chr6:133550279-133631190	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886679	chr6:133578733-133635272	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs402020	TAAR2	cis	cerebellum	SCAN
rs402020	SNORD101	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133594200-133612800	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:133594200-133614000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:133594200-133617200	Weak transcription	Left Ventricle	heart
4	chr6:133599000-133610400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:133599000-133629000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:133599800-133612400	Weak transcription	A549	lung
7	chr6:133605600-133614000	Weak transcription	Psoas Muscle	Psoas
8	chr6:133607200-133611000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:133607400-133609600	Weak transcription	Hela-S3	cervix
10	chr6:133608400-133609800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:133608600-133609600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:133608600-133611600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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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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