Variant report

Variant	rs1878269
Chromosome Location	chr3:56479466-56479467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1388255	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1491163	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1552668	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1552669	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35139577	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4527348	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974214	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58145335	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445790	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445792	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6762660	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6783666	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6784781	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6785094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796830	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6807444	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs725089	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7628279	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7637479	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7644198	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7646515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975582	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812701	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9829542	0.95[EUR][1000 genomes]
rs9856358	0.95[EUR][1000 genomes]
rs9871408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1878269	ERC2	cis	cerebellum	SCAN
rs1878269	C3orf51	cis	cerebellum	SCAN

Chromatin state (count:7 , 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	chr3:56469000-56481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:56469000-56492600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:56478000-56486800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:56479000-56480400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:56479400-56480000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:56479400-56480200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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