Variant report

Variant	rs1789650
Chromosome Location	chr11:93932461-93932462
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR83-2	chr11:93932429-93932509	XLOC_009524
2	lnc-GPR83-2	chr11:93932428-93932509	NONHSAT023709

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1014500	0.83[AMR][1000 genomes]
rs10444216	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1046805	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1046812	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1070	0.92[CEU][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10765655	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10765656	0.85[AMR][1000 genomes]
rs11020675	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11605491	0.85[AMR][1000 genomes]
rs1540177	0.85[AMR][1000 genomes]
rs16920011	0.85[AMR][1000 genomes]
rs1789653	0.87[AMR][1000 genomes]
rs1789655	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792624	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792634	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs1857681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1893808	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1893809	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3020014	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3020015	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3020017	0.84[AMR][1000 genomes]
rs625080	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs659288	0.86[AMR][1000 genomes];0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1789650	PANX1	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93917600-93934200	Weak transcription	Fetal Intestine Small	intestine
2	chr11:93920400-93933000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:93920400-93937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:93926800-93938800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:93927600-93932600	Weak transcription	NH-A	brain
6	chr11:93928600-93933000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:93928600-93934200	Weak transcription	HSMMtube	muscle
8	chr11:93929400-93934000	Enhancers	NHDF-Ad	bronchial
9	chr11:93929400-93935400	Enhancers	NHLF	lung
10	chr11:93930200-93934000	Weak transcription	Liver	Liver
11	chr11:93930400-93935200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:93931600-93934400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:93931800-93933200	Enhancers	Fetal Lung	lung
14	chr11:93932000-93933600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:93932000-93934000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:93932000-93934200	Enhancers	A549	lung
17	chr11:93932000-93936400	Enhancers	HepG2	liver
18	chr11:93932200-93933200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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