Variant report

Variant	rs1792634
Chromosome Location	chr11:93929510-93929511
allele	A/C
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:
2	chr11:93929115..93931956-chr11:94225381..94228826,3	K562	blood:

Variant related genes	Relation type
ENSG00000020922	Chromatin interaction
ENSG00000168876	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1014500	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10444216	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs1046805	0.91[MEX][hapmap];0.86[AMR][1000 genomes]
rs1046812	0.86[MEX][hapmap];0.86[AMR][1000 genomes]
rs1070	0.91[MEX][hapmap];0.84[AMR][1000 genomes]
rs10765656	0.84[ASN][1000 genomes]
rs11020675	0.86[AMR][1000 genomes]
rs11605491	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1540177	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16920011	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1789650	0.86[AMR][1000 genomes]
rs1789652	0.86[YRI][hapmap]
rs1789653	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792624	0.82[AMR][1000 genomes]
rs1857681	0.80[CEU][hapmap];0.84[AMR][1000 genomes]
rs1893808	0.85[AMR][1000 genomes]
rs1893809	0.81[CEU][hapmap];0.85[AMR][1000 genomes]
rs3020014	0.80[AMR][1000 genomes]
rs3020015	0.84[AMR][1000 genomes]
rs3020017	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1792634	SCARNA9	cis	parietal	SCAN
rs1792634	PANX1	cis	lymphoblastoid	seeQTL
rs1792634	C11orf54	cis	parietal	SCAN
rs1792634	RP11-680H20.2	cis	Artery Tibial	GTEx

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	chr11:93926600-93929600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:93926800-93932200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr11:93926800-93938800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:93927200-93929600	Weak transcription	A549	lung
8	chr11:93927400-93929800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:93927600-93932600	Weak transcription	NH-A	brain
10	chr11:93928600-93933000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:93928600-93934200	Weak transcription	HSMMtube	muscle
12	chr11:93929400-93929800	Enhancers	Stomach Mucosa	stomach
13	chr11:93929400-93930000	Enhancers	Pancreas	Pancrea
14	chr11:93929400-93930200	Enhancers	Liver	Liver
15	chr11:93929400-93930200	Enhancers	Gastric	stomach
16	chr11:93929400-93931200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:93929400-93934000	Enhancers	NHDF-Ad	bronchial
18	chr11:93929400-93935400	Enhancers	NHLF	lung

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