Variant report

Variant	rs2878806
Chromosome Location	chr11:17713507-17713508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17705084..17707821-chr11:17711837..17714694,2	K562	blood:
2	chr11:17710440..17715421-chr11:17715832..17719362,5	K562	blood:

Variant related genes	Relation type
ENSG00000254586	Chromatin interaction
ENSG00000255335	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10766416	0.84[EUR][1000 genomes]
rs10766418	0.86[ASN][1000 genomes]
rs10766419	0.88[ASN][1000 genomes]
rs10766420	0.82[EUR][1000 genomes]
rs10766423	0.86[EUR][1000 genomes]
rs10832837	0.85[ASN][1000 genomes]
rs10832841	0.83[ASN][1000 genomes]
rs10832842	0.84[EUR][1000 genomes]
rs11024364	0.85[ASN][1000 genomes]
rs11024367	0.85[ASN][1000 genomes]
rs11024368	0.85[ASN][1000 genomes]
rs11024375	0.86[ASN][1000 genomes]
rs12785437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16934571	0.81[ASN][1000 genomes]
rs28609365	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28683112	0.95[ASN][1000 genomes]
rs2878807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858493	0.85[EUR][1000 genomes]
rs3858494	0.85[EUR][1000 genomes]
rs3858495	0.85[EUR][1000 genomes]
rs3858496	0.85[EUR][1000 genomes]
rs3858498	0.85[EUR][1000 genomes]
rs3858499	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858506	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs3858507	0.87[EUR][1000 genomes]
rs3901226	0.80[CEU][hapmap]
rs3901370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911833	0.80[CEU][hapmap]
rs3928366	0.85[EUR][1000 genomes]
rs4081578	0.87[ASW][hapmap]
rs4141260	0.88[ASN][1000 genomes]
rs4141261	0.85[ASN][1000 genomes]
rs4756905	0.85[ASN][1000 genomes]
rs4756907	0.88[ASN][1000 genomes]
rs4756910	0.86[EUR][1000 genomes]
rs4756912	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs4757565	0.86[ASN][1000 genomes]
rs4757567	0.88[ASN][1000 genomes]
rs4757568	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.92[YRI][hapmap];0.95[ASN][1000 genomes]
rs4757569	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.95[ASN][1000 genomes]
rs4757570	0.90[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs6416178	0.86[EUR][1000 genomes]
rs6486390	0.86[EUR][1000 genomes]
rs7101870	0.80[EUR][1000 genomes]
rs7106809	0.82[EUR][1000 genomes]
rs7109072	0.90[CEU][hapmap]
rs7123420	0.86[EUR][1000 genomes]
rs7128599	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7395942	0.83[ASN][1000 genomes]
rs7478812	0.82[EUR][1000 genomes]
rs7937727	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040065	chr11:17556031-17753467	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1044126	chr11:17557715-17730646	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv540953	chr11:17557715-17730646	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv467717	chr11:17713507-17791822	Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv553588	chr11:17713507-17791822	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2878806	SNORA21	trans	cerebellum	SCAN
rs2878806	CACNA1F	trans	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17711200-17714400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr11:17712600-17714000	Enhancers	HSMM	muscle
3	chr11:17712800-17714400	Enhancers	Fetal Muscle Leg	muscle
4	chr11:17712800-17716000	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr11:17713200-17713600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr11:17713200-17718000	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr11:17713200-17721800	Enhancers	Psoas Muscle	Psoas
8	chr11:17713400-17717200	Enhancers	HSMMtube	muscle

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