Variant report

Variant	rs1878270
Chromosome Location	chr3:56487580-56487581
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1388257	0.82[AMR][1000 genomes]
rs1491169	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1552671	0.83[AMR][1000 genomes]
rs1878267	0.85[EUR][1000 genomes]
rs1878268	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2317065	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6776781	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs885211	0.84[ASN][1000 genomes]
rs923654	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9311602	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9819137	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831365	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9853704	0.82[AMR][1000 genomes]
rs9855289	0.81[CEU][hapmap];0.80[MEX][hapmap]
rs9858744	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9873381	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1878270	ERC2	cis	cerebellum	SCAN
rs1878270	C3orf51	cis	cerebellum	SCAN
rs1878270	ITIH1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56469000-56492600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:56487200-56488000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:56487200-56492600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:56487200-56492600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:56487400-56492200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:56487400-56492400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:56487400-56492600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:56487400-56492600	Weak transcription	iPS-15b 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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