Variant report

Variant	rs4488791
Chromosome Location	chr3:155925898-155925899
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155925817..155926573-chr5:116060845..116061700,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1118418	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1120745	0.93[ASN][1000 genomes]
rs11713991	0.86[ASN][1000 genomes]
rs11915771	0.84[ASN][1000 genomes]
rs11915832	0.93[ASN][1000 genomes]
rs11922447	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1353812	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1391889	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1391890	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs1499051	0.93[ASN][1000 genomes]
rs1499052	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499054	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499056	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs1546229	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs1909372	0.98[ASN][1000 genomes]
rs1909373	0.93[ASN][1000 genomes]
rs1909374	0.93[ASN][1000 genomes]
rs1909375	0.90[ASN][1000 genomes]
rs1909376	0.93[ASN][1000 genomes]
rs2173492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3936002	1.00[JPT][hapmap]
rs4258915	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4271877	0.93[ASN][1000 genomes]
rs4333049	0.93[ASN][1000 genomes]
rs4355235	0.90[ASN][1000 genomes]
rs4450760	0.84[ASN][1000 genomes]
rs4453801	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4505650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4530487	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs4533601	1.00[JPT][hapmap]
rs4577423	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4580504	1.00[JPT][hapmap]
rs4634068	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4679763	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679764	0.93[ASN][1000 genomes]
rs4679765	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680238	0.90[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs4680239	1.00[JPT][hapmap]
rs4680249	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs6441045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441046	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6441047	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441050	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[ASN][1000 genomes]
rs6441051	0.93[ASN][1000 genomes]
rs6775600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784723	1.00[JPT][hapmap]
rs6788238	0.93[ASN][1000 genomes]
rs6806129	0.98[ASN][1000 genomes]
rs728382	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs7372394	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611194	0.88[ASN][1000 genomes]
rs7612532	0.91[ASN][1000 genomes]
rs7621586	0.93[ASN][1000 genomes]
rs7627105	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7633871	0.93[ASN][1000 genomes]
rs7634800	0.93[ASN][1000 genomes]
rs7638421	0.93[ASN][1000 genomes]
rs7640712	0.93[ASN][1000 genomes]
rs9289962	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9818040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857202	0.93[ASN][1000 genomes]
rs9864967	0.90[ASN][1000 genomes]
rs9866991	1.00[CHB][hapmap];0.93[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	nsv592085	chr3:155827634-156012679	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4488791	SCARNA7	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155918200-155928400	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:155919600-155926000	Weak transcription	Aorta	Aorta
3	chr3:155920200-155926000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:155922600-155929800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:155923600-155926000	Enhancers	Osteobl	bone
6	chr3:155923600-155927000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:155923800-155926600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:155924000-155926800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:155924800-155926800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:155925200-155926000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:155925200-155929000	Weak transcription	HMEC	breast
12	chr3:155925400-155926400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:155925400-155926600	Enhancers	HSMMtube	muscle
14	chr3:155925600-155929800	Enhancers	Fetal Heart	heart
15	chr3:155925800-155926400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:155925800-155926400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:155925800-155926600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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