Variant report

Variant	rs6729866
Chromosome Location	chr2:55118078-55118079
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10164641	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13383645	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385982	0.85[ASN][1000 genomes]
rs13408207	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13410462	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1432104	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17346032	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1898699	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545453	0.81[AFR][1000 genomes]
rs6545454	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718267	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6746577	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72482058	0.91[ASN][1000 genomes]
rs7355309	0.84[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs7595599	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9309260	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997198	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][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	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6729866	TSPYL6	cis	cerebellum	SCAN
rs6729866	PSME4	cis	parietal	SCAN
rs6729866	CCDC85A	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55068600-55122400	Weak transcription	Brain Anterior Caudate	brain
2	chr2:55081400-55122400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:55087800-55126000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:55095200-55148200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:55106600-55124000	Weak transcription	Spleen	Spleen
6	chr2:55107400-55122600	Weak transcription	Brain Substantia Nigra	brain
7	chr2:55109200-55126800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:55109200-55127600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:55111600-55122400	Weak transcription	HepG2	liver
10	chr2:55115400-55121800	Weak transcription	Aorta	Aorta

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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