Variant report

Variant	rs152602
Chromosome Location	chr5:106776118-106776119
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:106775777..106777698-chr5:106792943..106795923,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs115779	0.94[ASN][1000 genomes]
rs149444	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs149498	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs151956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs151958	0.95[ASN][1000 genomes]
rs152582	0.89[ASN][1000 genomes]
rs152584	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs152585	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs152587	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs152589	0.91[ASN][1000 genomes]
rs152590	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs152591	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs152592	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs152593	0.95[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs152595	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs152596	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs152597	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs152598	0.97[ASN][1000 genomes]
rs152599	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs152601	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs152603	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152605	0.97[ASN][1000 genomes]
rs152606	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs152607	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs152608	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs152609	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs152611	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs152612	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152613	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs153686	0.99[ASN][1000 genomes]
rs154645	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs154646	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs154647	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs154648	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2283	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs252991	0.88[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs27661	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3843490	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs152602	FER	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106758600-106785000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:106768600-106778800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:106768600-106779000	Weak transcription	HSMM	muscle
4	chr5:106772600-106779000	Weak transcription	Left Ventricle	heart
5	chr5:106772600-106790800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:106773200-106782800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:106773400-106777400	Enhancers	Fetal Heart	heart
8	chr5:106773600-106776600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:106774400-106776600	ZNF genes & repeats	A549	lung
10	chr5:106774600-106779800	Weak transcription	Brain Germinal Matrix	brain
11	chr5:106774600-106785000	Weak transcription	Fetal Lung	lung
12	chr5:106774600-106790600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:106775400-106777000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:106775400-106781600	Weak transcription	Aorta	Aorta
15	chr5:106775600-106781200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:106776000-106781000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links