Variant report

Variant	rs12467381
Chromosome Location	chr2:55116496-55116497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10171653	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10201734	0.85[ASN][1000 genomes]
rs17046477	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34121514	0.87[EUR][1000 genomes]
rs36126551	0.93[EUR][1000 genomes]
rs4671987	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671988	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671989	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4671990	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4671991	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60808665	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6545456	0.85[ASN][1000 genomes]
rs6707572	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67299431	0.87[EUR][1000 genomes]
rs7355716	0.92[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs919669	0.97[AMR][1000 genomes];0.95[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12467381	CCDC88A	cis	cerebellum	SCAN
rs12467381	C2orf73	cis	parietal	SCAN
rs12467381	ERLEC1	cis	parietal	SCAN
rs12467381	CCDC104	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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