Variant report

Variant	rs9290998
Chromosome Location	chr3:191401581-191401582
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	chr3:191401415..191403217-chr3:191403592..191405646,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11712348	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713378	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13089779	1.00[ASN][1000 genomes]
rs13323801	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13433981	0.83[EUR][1000 genomes]
rs1464649	0.83[EUR][1000 genomes]
rs1464650	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1464651	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2365534	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2886486	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4393947	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4434185	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687226	0.82[EUR][1000 genomes]
rs4687235	0.83[EUR][1000 genomes]
rs4687237	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687251	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687252	1.00[ASN][1000 genomes]
rs57196585	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57290773	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57667341	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762390	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73204638	0.83[EUR][1000 genomes]
rs73204640	0.83[EUR][1000 genomes]
rs73204641	0.92[ASN][1000 genomes]
rs73204644	0.83[EUR][1000 genomes]
rs73204669	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433470	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7633696	1.00[ASN][1000 genomes]
rs7651123	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs9816423	0.83[EUR][1000 genomes]
rs9825110	0.94[EUR][1000 genomes]
rs9834613	0.82[EUR][1000 genomes]
rs9840419	1.00[ASN][1000 genomes]
rs9844704	0.88[EUR][1000 genomes]
rs9846006	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9863483	0.96[ASN][1000 genomes]
rs9875132	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9879803	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9882196	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915689	chr3:191244719-191479974	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv997817	chr3:191284834-191475809	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1001082	chr3:191320636-191579587	Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1009378	chr3:191359361-191928703	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1000060	chr3:191359361-191935048	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1002406	chr3:191380544-191404841	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv1002112	chr3:191395769-191471002	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv461121	chr3:191395972-191431496	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv592854	chr3:191395972-191431496	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9290998	FGF12	cis	cerebellum	SCAN
rs9290998	PPP1R2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191390800-191406400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:191392200-191404400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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