Variant report

Variant	rs11130098
Chromosome Location	chr3:46661926-46661927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs11130100	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11709020	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11709936	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11710264	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719679	0.82[CEU][hapmap]
rs12330414	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491236	0.82[CEU][hapmap]
rs12491294	0.82[CEU][hapmap]
rs13319345	0.84[ASN][1000 genomes]
rs1520487	0.92[ASN][1000 genomes]
rs2385858	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891885	0.92[ASN][1000 genomes]
rs3796371	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442010	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6774048	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs6805749	0.87[ASN][1000 genomes]
rs7610008	0.89[ASN][1000 genomes]
rs7633770	0.81[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs877680	0.82[CEU][hapmap]
rs877681	0.82[CEU][hapmap]

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	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv876738	chr3:46639048-46680063	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11130098	GNAI2	cis	cerebellum	SCAN
rs11130098	C3orf39	cis	cerebellum	SCAN
rs11130098	LRRC2	cis	cerebellum	SCAN
rs11130098	ALS2CL	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46651600-46671200	Weak transcription	Right Atrium	heart
2	chr3:46654400-46663000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:46661200-46662400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:46661200-46662400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:46661400-46662000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:46661400-46662000	Enhancers	Adipose Nuclei	Adipose
7	chr3:46661400-46662400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:46661600-46662200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:46661600-46662200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:46661600-46662200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:46661600-46670200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:46661800-46666200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:46661800-46666600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:46661800-46670200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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