Variant report

Variant	rs2054878
Chromosome Location	chr3:155680468-155680469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155679304..155682276-chr3:155682932..155686695,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10804773	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10804774	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10936020	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1131925	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs11706359	0.88[CEU][hapmap]
rs11714133	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13061037	0.81[CEU][hapmap]
rs13065994	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13091683	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13096499	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2063903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2200707	0.85[CEU][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34337666	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35321137	0.88[ASN][1000 genomes]
rs35472369	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358703	0.91[MEX][hapmap]
rs3772115	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3772116	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821365	0.87[ASN][1000 genomes]
rs4680219	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680223	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441028	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs66509404	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6763830	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6799267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6804740	0.85[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6809229	0.92[CEU][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs7619976	0.85[ASN][1000 genomes]
rs7629523	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7633168	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7643630	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7651038	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7652005	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs965035	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[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	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2753744	chr3:155487298-155707298	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2054878	RARRES1	cis	cerebellum	SCAN
rs2054878	SLC33A1	cis	cerebellum	SCAN
rs2054878	SLC33A1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155660400-155688000	Weak transcription	Hela-S3	cervix
2	chr3:155664600-155681200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:155674200-155681600	Weak transcription	NH-A	brain
4	chr3:155677800-155681200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:155678000-155681400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:155678400-155681400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:155679600-155688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:155680400-155682200	Enhancers	Osteobl	bone
9	chr3:155680400-155684200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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