Variant report

Variant	rs1878268
Chromosome Location	chr3:56479363-56479364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1491169	0.86[ASN][1000 genomes]
rs1878267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1878270	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2317065	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6776781	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs923654	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9311602	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9819137	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9831365	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9855289	0.85[ASW][hapmap];0.89[CHB][hapmap];0.88[MEX][hapmap];0.84[AFR][1000 genomes]
rs9858744	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9873381	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9876092	0.84[AFR][1000 genomes]
rs9876122	0.84[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	esv3383044	chr3:56466497-56483664	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1878268	C3orf78	cis	parietal	SCAN
rs1878268	ERC2	cis	cerebellum	SCAN
rs1878268	ITIH1	cis	cerebellum	SCAN
rs1878268	C3orf51	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56456400-56479600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:56469000-56479400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:56469000-56481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:56469000-56492600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:56478000-56486800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:56479000-56480400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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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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