Variant report

Variant	rs11020679
Chromosome Location	chr11:93928787-93928788
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	chr11:93928773..93931046-chr11:93935026..93936548,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1014499	0.96[EUR][1000 genomes]
rs10458852	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10765657	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10765658	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10765660	0.96[EUR][1000 genomes]
rs10831169	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10831173	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10831174	0.93[EUR][1000 genomes]
rs10831176	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10831184	0.93[EUR][1000 genomes]
rs11020678	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11020703	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11020719	0.85[EUR][1000 genomes]
rs12366039	0.96[EUR][1000 genomes]
rs12792677	0.96[EUR][1000 genomes]
rs12808853	0.96[EUR][1000 genomes]
rs1361929	0.81[EUR][1000 genomes]
rs1541301	0.96[CEU][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16920039	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1789652	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1792632	0.84[EUR][1000 genomes]
rs1857680	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1944436	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2000956	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2156627	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3020004	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3020016	0.88[CEU][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes]
rs4597032	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4753131	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4753132	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs480710	0.93[EUR][1000 genomes]
rs581771	0.93[EUR][1000 genomes]
rs613234	0.93[EUR][1000 genomes]
rs655358	0.85[EUR][1000 genomes]
rs689315	0.93[EUR][1000 genomes]
rs7115129	0.81[EUR][1000 genomes]
rs7118270	0.93[EUR][1000 genomes]
rs7130456	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7927338	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7927496	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7936241	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898184	chr11:93741612-93969726	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1046092	chr11:93833446-93964452	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv469980	chr11:93864321-93962121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv468795	chr11:93864321-93964917	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv555966	chr11:93864321-93964917	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1038294	chr11:93918837-93982605	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11020679	PANX1	cis	lymphoblastoid	seeQTL
rs11020679	GPR83	cis	parietal	SCAN
rs11020679	PANX1	cis	parietal	SCAN
rs11020679	GPR83	cis	cerebellum	SCAN
rs11020679	C11orf54	cis	parietal	SCAN
rs11020679	MRE11A	cis	parietal	SCAN
rs11020679	RP11-680H20.2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93913600-93929400	Weak transcription	Gastric	stomach
2	chr11:93915600-93929400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:93917600-93934200	Weak transcription	Fetal Intestine Small	intestine
4	chr11:93920400-93929400	Weak transcription	Pancreas	Pancrea
5	chr11:93920400-93933000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:93920400-93937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:93926600-93929600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr11:93926800-93932200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:93926800-93938800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:93927000-93929400	Weak transcription	NHDF-Ad	bronchial
11	chr11:93927200-93929400	Weak transcription	NHLF	lung
12	chr11:93927200-93929600	Weak transcription	A549	lung
13	chr11:93927400-93929400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:93927400-93929800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr11:93927600-93932600	Weak transcription	NH-A	brain
16	chr11:93928600-93933000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:93928600-93934200	Weak transcription	HSMMtube	muscle

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