Variant report

Variant	rs10892620
Chromosome Location	chr11:120587319-120587320
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10892618	0.80[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes]
rs10892619	0.81[AMR][1000 genomes]
rs17245664	0.81[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]
rs3133855	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3133856	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054407	chr11:120535570-120630114	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1053607	chr11:120540795-120802006	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3693392	chr11:120549745-120628012	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1041465	chr11:120582595-120630114	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv541180	chr11:120582595-120630114	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv1038264	chr11:120582595-120799335	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv541181	chr11:120582595-120799335	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv832286	chr11:120585843-120745846	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10892620	ATP5L	cis	cerebellum	SCAN
rs10892620	ARHGEF12	cis	lymphoblastoid	seeQTL
rs10892620	FXYD6	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120582200-120588800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr11:120585800-120588600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr11:120585800-120590000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:120586200-120587600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:120586200-120588600	Enhancers	Ovary	ovary
6	chr11:120586200-120590000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr11:120586400-120588400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:120586400-120588600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:120586400-120588600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr11:120586400-120588800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:120586400-120593200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:120586600-120588600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr11:120586600-120590400	Weak transcription	Fetal Intestine Large	intestine
14	chr11:120586800-120587800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:120586800-120587800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:120586800-120587800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:120587000-120587800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:120587200-120587800	Enhancers	Colon Smooth Muscle	Colon
19	chr11:120587200-120589600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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