Variant report

Variant	rs747559
Chromosome Location	chr4:103414175-103414176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103412095..103417199-chr4:103420404..103424320,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1005819	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1020759	0.96[CEU][hapmap]
rs1020760	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs11722146	0.91[JPT][hapmap]
rs11723120	0.90[JPT][hapmap]
rs11733168	0.86[YRI][hapmap]
rs118882	0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs12509517	0.91[JPT][hapmap]
rs1585213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs1585215	1.00[JPT][hapmap]
rs1598856	0.84[CHD][hapmap]
rs1598859	0.91[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1599961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs17032705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs170731	1.00[JPT][hapmap]
rs1801	0.91[JPT][hapmap]
rs1882949	0.86[YRI][hapmap]
rs2085548	0.85[CHD][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap]
rs2168805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs230491	1.00[JPT][hapmap]
rs230492	1.00[JPT][hapmap]
rs230493	1.00[JPT][hapmap];0.85[TSI][hapmap]
rs230495	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230496	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230498	1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs230500	1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs230504	0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs230505	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs230509	1.00[JPT][hapmap]
rs230514	1.00[JPT][hapmap]
rs230515	1.00[JPT][hapmap]
rs230516	1.00[JPT][hapmap]
rs230519	0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs230520	0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs230521	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230525	1.00[JPT][hapmap];0.80[TSI][hapmap]
rs230526	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs230528	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs230529	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs230531	0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs230532	0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs230533	1.00[JPT][hapmap]
rs230534	1.00[JPT][hapmap]
rs230535	0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs230539	0.95[JPT][hapmap]
rs230540	0.91[JPT][hapmap]
rs230541	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs230542	0.91[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs3755867	0.91[JPT][hapmap]
rs3774933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774936	1.00[JPT][hapmap]
rs3774937	0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs3774938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774956	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs3774959	0.91[JPT][hapmap];0.83[TSI][hapmap]
rs3774963	0.90[JPT][hapmap]
rs3774964	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4235404	1.00[JPT][hapmap]
rs4648011	0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs4648055	0.91[JPT][hapmap]
rs4648058	0.90[JPT][hapmap]
rs4648068	0.91[JPT][hapmap]
rs4698858	0.95[CEU][hapmap];0.89[JPT][hapmap]
rs4699030	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs9790601	0.91[JPT][hapmap]
rs980455	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs9996514	0.89[YRI][hapmap]

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	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs747559	MAPKSP1	cis	cerebellum	SCAN
rs747559	MANBA	cis	multi-tissue	Pritchard
rs747559	COL9A2	trans	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103399600-103416000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:103412800-103414200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr4:103412800-103414600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:103413200-103415000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr4:103413200-103415200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:103413600-103414800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:103413600-103415200	Enhancers	HMEC	breast
8	chr4:103413800-103415200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:103413800-103415200	Enhancers	NHEK	skin
10	chr4:103413800-103416000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:103413800-103418400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:103414000-103414600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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