Variant report

Variant	rs12605978
Chromosome Location	chr18:45570094-45570095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs4245250	0.82[EUR][1000 genomes]
rs4245251	0.82[EUR][1000 genomes]
rs4359513	0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs4620750	0.85[YRI][hapmap]
rs4939701	0.92[LWK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs7230700	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs8093883	0.85[YRI][hapmap]
rs9959819	0.86[EUR][1000 genomes];0.82[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	nsv909616	chr18:45467806-45844500	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12605978	SIGLEC15	cis	cerebellum	SCAN
rs12605978	SMAD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45558400-45578400	Weak transcription	Ovary	ovary
2	chr18:45564400-45576000	Weak transcription	Stomach Mucosa	stomach
3	chr18:45564800-45572000	Weak transcription	Placenta	Placenta
4	chr18:45566600-45576200	Weak transcription	Hela-S3	cervix
5	chr18:45567200-45572200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr18:45567200-45576800	Weak transcription	Colonic Mucosa	Colon
7	chr18:45567400-45571800	Weak transcription	Gastric	stomach
8	chr18:45567400-45576200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr18:45567600-45570400	Weak transcription	Spleen	Spleen
10	chr18:45567600-45573000	Weak transcription	Aorta	Aorta
11	chr18:45567600-45576400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr18:45567800-45572000	Weak transcription	Esophagus	oesophagus
13	chr18:45568000-45571200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr18:45568000-45573200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr18:45569000-45575600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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