Variant report

Variant	rs9645830
Chromosome Location	chr12:72839822-72839823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 48 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10160913	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10506655	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs10879429	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10879430	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10879431	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10879432	0.86[EUR][1000 genomes]
rs10879433	0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs11179183	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11179189	0.92[EUR][1000 genomes]
rs11179192	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11179199	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11608809	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs12297047	0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs12301567	1.00[CEU][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12372580	0.90[EUR][1000 genomes]
rs1444602	0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs17111103	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs17111240	0.80[EUR][1000 genomes]
rs725409	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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	15 gene(s)	inside rSNPs	diseases
6	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv832453	chr12:72778058-72966827	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv772	chr12:72809902-72852196	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv817280	chr12:72820558-73508605	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv521839	chr12:72827033-72839822	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv469466	chr12:72830441-72885554	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv559364	chr12:72830441-72885554	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:48)

SNP	Gene	Cis/trans	Tissue	Source
rs9645830	APBA2	cis	Temporal Cortex	GTEx
rs9645830	NUPR1	cis	Temporal Cortex	GTEx
rs9645830	COPG	cis	Temporal Cortex	GTEx
rs9645830	EEF1D	cis	Temporal Cortex	GTEx
rs9645830	ATP5I	cis	Temporal Cortex	GTEx
rs9645830	CADM3	cis	Temporal Cortex	GTEx
rs9645830	SAMD9L	cis	Temporal Cortex	GTEx
rs9645830	VIPR1	cis	Temporal Cortex	GTEx
rs9645830	SFRS14	cis	Temporal Cortex	GTEx
rs9645830	GIMAP8	cis	Temporal Cortex	GTEx
rs9645830	SERBP1	cis	Temporal Cortex	GTEx
rs9645830	GSDMD	cis	Temporal Cortex	GTEx
rs9645830	CNTNAP1	cis	Temporal Cortex	GTEx
rs9645830	C9orf45	cis	Temporal Cortex	GTEx
rs9645830	RPL6	cis	Temporal Cortex	GTEx
rs9645830	RPS29	cis	Temporal Cortex	GTEx
rs9645830	DBC1	cis	Temporal Cortex	GTEx
rs9645830	FCHSD2	cis	Temporal Cortex	GTEx
rs9645830	PODN	cis	Temporal Cortex	GTEx
rs9645830	DNM1	cis	Temporal Cortex	GTEx
rs9645830	USP11	cis	Temporal Cortex	GTEx
rs9645830	DUSP23	cis	Temporal Cortex	GTEx
rs9645830	GAP43	cis	Temporal Cortex	GTEx
rs9645830	POLR3GL	cis	Temporal Cortex	GTEx
rs9645830	NRSN2	cis	Temporal Cortex	GTEx
rs9645830	ANKRD57	cis	Temporal Cortex	GTEx
rs9645830	DLGAP2	cis	Temporal Cortex	GTEx
rs9645830	ARL3	cis	Temporal Cortex	GTEx
rs9645830	LPHN1	cis	Temporal Cortex	GTEx
rs9645830	GNPDA1	cis	Temporal Cortex	GTEx
rs9645830	PKNOX2	cis	Temporal Cortex	GTEx
rs9645830	RPS8	cis	Temporal Cortex	GTEx
rs9645830	UNC5A	cis	Temporal Cortex	GTEx
rs9645830	HERC5	cis	Temporal Cortex	GTEx
rs9645830	ZNF280B	cis	Temporal Cortex	GTEx
rs9645830	MYL6	cis	Temporal Cortex	GTEx
rs9645830	SIPA1	cis	Temporal Cortex	GTEx
rs9645830	MUTED	cis	Temporal Cortex	GTEx
rs9645830	C12orf75	cis	Temporal Cortex	GTEx
rs9645830	CUGBP2	cis	Temporal Cortex	GTEx
rs9645830	GIMAP4	cis	Temporal Cortex	GTEx
rs9645830	ACVR1B	cis	Temporal Cortex	GTEx
rs9645830	TM9SF4	cis	Temporal Cortex	GTEx
rs9645830	PPFIA2	cis	Temporal Cortex	GTEx
rs9645830	BST2	cis	Temporal Cortex	GTEx
rs9645830	SLC15A3	cis	Temporal Cortex	GTEx
rs9645830	PRRT3	cis	Temporal Cortex	GTEx
rs9645830	NEFL	cis	Temporal Cortex	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72831200-72847400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:72838800-72842000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:72839000-72842600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:72839400-72842800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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