Variant report

Variant	rs2121468
Chromosome Location	chr11:92932229-92932230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr11:92929964-92932450	HL-60	blood:	n/a	chr11:92931581-92931601 chr11:92931403-92931412 chr11:92931589-92931599 chr11:92931587-92931601 chr11:92931581-92931601 chr11:92931581-92931601

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:92922677..92925407-chr11:92931500..92933970,2	K562	blood:

Variant related genes	Relation type
SLC36A4	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10466352	0.84[GIH][hapmap];0.81[JPT][hapmap]
rs10765587	0.88[GIH][hapmap];0.81[JPT][hapmap]
rs10765593	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10830988	0.83[GIH][hapmap];0.87[JPT][hapmap]
rs10830989	0.86[GIH][hapmap];0.81[JPT][hapmap]
rs10830996	0.86[GIH][hapmap];0.81[JPT][hapmap]
rs10831010	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10831016	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10831017	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11020195	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11020229	0.86[AMR][1000 genomes]
rs11020234	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11020235	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12099012	0.85[AMR][1000 genomes]
rs12803876	0.87[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes]
rs12808030	0.80[AMR][1000 genomes]
rs1348871	0.81[JPT][hapmap]
rs1446904	0.84[AMR][1000 genomes]
rs1446920	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1508608	0.86[GIH][hapmap];0.81[JPT][hapmap]
rs1992803	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4753436	0.86[GIH][hapmap];0.81[JPT][hapmap]
rs55818036	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6483228	0.85[AMR][1000 genomes]
rs7925288	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935450	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039134	chr11:92790000-93219942	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv898176	chr11:92877533-92965312	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv898177	chr11:92877533-92971874	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv898178	chr11:92881933-92949447	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv898179	chr11:92881933-92956873	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv818858	chr11:92898342-92932229	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	esv2757465	chr11:92898342-92934137	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	esv2759853	chr11:92898342-92934137	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	esv2829957	chr11:92915544-92932229	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	esv33564	chr11:92918600-92936545	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2121468	SNORA1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:92931400-92933600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr11:92932000-92932400	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr11:92932000-92932400	Enhancers	Brain Germinal Matrix	brain
4	chr11:92932000-92933000	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:92932000-92933200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:92932000-92934200	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr11:92932000-92934400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr11:92932200-92932600	Weak transcription	Primary B cells from cord blood	blood
9	chr11:92932200-92932600	Enhancers	Brain Anterior Caudate	brain

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