Variant report

Variant	rs6550879
Chromosome Location	chr3:24622893-24622894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24535513..24537264-chr3:24622149..24624564,2	MCF-7	breast:
2	chr3:24622288..24625025-chr3:24625704..24628070,2	K562	blood:
3	chr3:24535816..24538509-chr3:24621418..24627791,6	MCF-7	breast:
4	chr3:24619219..24620800-chr3:24620874..24623733,3	K562	blood:
5	chr3:24535255..24538695-chr3:24622610..24625331,3	K562	blood:

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10212332	0.98[ASN][1000 genomes]
rs10490837	0.93[CHB][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs11712286	0.88[CEU][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13318800	0.86[ASN][1000 genomes]
rs1561079	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17014900	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs17014902	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs1992040	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1992041	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2043578	0.82[EUR][1000 genomes]
rs2117873	0.87[ASN][1000 genomes]
rs2196434	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2196438	0.96[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs28562279	0.92[ASN][1000 genomes]
rs3919672	0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap]
rs56268655	0.86[ASN][1000 genomes]
rs58152527	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61701305	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550878	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767534	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6767717	0.99[ASN][1000 genomes]
rs6769209	0.96[ASN][1000 genomes]
rs6770518	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6771818	0.96[ASN][1000 genomes]
rs6781066	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6795607	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6801494	0.99[ASN][1000 genomes]
rs73040438	0.87[ASN][1000 genomes]
rs7647700	0.86[ASN][1000 genomes]
rs930317	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9310745	0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs9819865	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9823545	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs9830859	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9835497	0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9838616	1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs9838720	1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs9843609	0.84[ASN][1000 genomes]
rs9844544	0.85[ASN][1000 genomes]
rs9850443	0.82[LWK][hapmap]
rs9850781	0.86[ASN][1000 genomes]
rs9853927	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs9859978	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9861129	0.84[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs9868375	0.89[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9873830	0.92[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9878606	0.85[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6550879	RPL15	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24617800-24623400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:24618000-24629600	Weak transcription	Right Atrium	heart
3	chr3:24621200-24623400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:24621200-24623400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:24621200-24624200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:24621200-24624200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:24621200-24633400	Weak transcription	K562	blood
8	chr3:24621400-24624200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:24621600-24627400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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