Variant report

Variant	rs7947588
Chromosome Location	chr11:10094405-10094406
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	chr11:10093616..10094485-chr4:5814395..5815135,2	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10128601	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10734652	0.83[ASN][1000 genomes]
rs10770080	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10770082	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10770083	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10770084	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10770085	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10770087	0.90[ASN][1000 genomes]
rs10770088	0.84[ASN][1000 genomes]
rs10770089	0.86[ASN][1000 genomes]
rs10770096	0.94[EUR][1000 genomes]
rs10770104	0.82[EUR][1000 genomes]
rs10840331	0.81[AMR][1000 genomes]
rs10840332	0.81[AMR][1000 genomes]
rs10840335	0.81[AMR][1000 genomes]
rs10840339	0.88[AMR][1000 genomes]
rs10840342	0.88[AMR][1000 genomes]
rs10840346	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10840349	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10840353	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10840354	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10840357	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10840358	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10840360	0.87[ASN][1000 genomes]
rs10840363	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10840365	0.86[ASN][1000 genomes]
rs10840368	0.83[ASN][1000 genomes]
rs11042581	0.88[AMR][1000 genomes]
rs11042582	0.88[AMR][1000 genomes]
rs11042598	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11042617	0.92[ASN][1000 genomes]
rs11042620	0.85[ASN][1000 genomes]
rs11042621	0.91[ASN][1000 genomes]
rs11042622	0.84[ASN][1000 genomes]
rs11042625	0.80[ASN][1000 genomes]
rs11042633	0.87[ASN][1000 genomes]
rs11042638	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11600852	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11602090	0.85[EUR][1000 genomes]
rs12224149	0.86[ASN][1000 genomes]
rs12288355	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12295754	0.88[AMR][1000 genomes]
rs12360854	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1442738	0.83[EUR][1000 genomes]
rs2083715	0.82[EUR][1000 genomes]
rs2083716	0.84[EUR][1000 genomes]
rs2083717	0.89[EUR][1000 genomes]
rs2403228	0.81[AMR][1000 genomes]
rs2403230	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2403259	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2403264	0.80[ASN][1000 genomes]
rs2403265	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2403268	0.86[EUR][1000 genomes]
rs4267063	0.88[EUR][1000 genomes]
rs4284389	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4309158	0.88[AMR][1000 genomes]
rs4316505	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4323860	0.92[EUR][1000 genomes]
rs4350354	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4366476	0.86[ASN][1000 genomes]
rs4466825	0.90[ASN][1000 genomes]
rs4482025	0.85[EUR][1000 genomes]
rs4509749	0.85[ASN][1000 genomes]
rs4635071	0.89[ASN][1000 genomes]
rs4909918	0.86[AMR][1000 genomes]
rs4910089	0.81[AMR][1000 genomes]
rs4910097	0.87[EUR][1000 genomes]
rs4910107	0.83[EUR][1000 genomes]
rs4910108	0.84[EUR][1000 genomes]
rs56063978	0.81[EUR][1000 genomes]
rs58623593	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6483860	0.80[AMR][1000 genomes]
rs6483883	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6483964	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6483965	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6483966	0.86[ASN][1000 genomes]
rs6483970	0.86[ASN][1000 genomes]
rs7102016	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7104821	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7106328	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7106491	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7106998	0.84[EUR][1000 genomes]
rs7110312	0.83[ASN][1000 genomes]
rs7110664	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7115944	0.83[EUR][1000 genomes]
rs7119000	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7121704	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7123728	0.91[EUR][1000 genomes]
rs7126376	0.80[ASN][1000 genomes]
rs7128591	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7128698	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7129239	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7131203	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs716803	0.81[EUR][1000 genomes]
rs7479039	0.84[EUR][1000 genomes]
rs7924499	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7928170	0.94[EUR][1000 genomes]
rs7932988	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7933482	0.80[AMR][1000 genomes]
rs7938543	0.82[EUR][1000 genomes]
rs7938891	0.92[ASN][1000 genomes]
rs7939146	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7942420	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7948166	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7950140	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7950240	0.87[AFR][1000 genomes];0.90[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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
2	nsv553476	chr11:10024311-10117435	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7947588	RP11-351I24.1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10072400-10101200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:10074000-10098200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:10085000-10098200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr11:10087800-10097800	Weak transcription	Right Atrium	heart
5	chr11:10090000-10098000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:10093200-10097600	Weak transcription	Fetal Intestine Small	intestine
7	chr11:10093400-10094800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:10093600-10094800	Enhancers	Osteobl	bone
9	chr11:10093800-10094600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:10094000-10098200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:10094200-10094600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:10094400-10097600	Weak transcription	Left Ventricle	heart

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