Variant report

Variant	rs9922786
Chromosome Location	chr16:12684696-12684697
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	chr16:12675875..12678223-chr16:12683631..12685864,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11075104	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11075105	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11075106	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11075111	0.98[ASN][1000 genomes]
rs11075124	0.82[GIH][hapmap]
rs11642724	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12918039	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12921676	0.84[ASN][1000 genomes]
rs12925724	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12926229	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12930615	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12934828	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2217269	0.81[ASN][1000 genomes]
rs2217270	0.81[ASN][1000 genomes]
rs2865576	0.85[ASN][1000 genomes]
rs3919631	0.81[ASN][1000 genomes]
rs4555141	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4781289	0.88[ASN][1000 genomes]
rs6498337	0.86[ASN][1000 genomes]
rs7184166	0.85[ASN][1000 genomes]
rs7193883	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7197638	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7197829	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7197841	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7198378	0.81[ASN][1000 genomes]
rs7198835	0.92[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.86[ASN][1000 genomes]
rs7199146	0.86[ASN][1000 genomes]
rs7203009	0.85[ASN][1000 genomes]
rs890903	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9635499	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription 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 miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv437802	chr16:12667076-12708294	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv571469	chr16:12670401-12715480	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv1804537	chr16:12671491-12708186	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv11602	chr16:12674207-12693522	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv18351	chr16:12674207-12734557	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv2756199	chr16:12676529-12705135	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv2757629	chr16:12676745-12712199	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv2758631	chr16:12676745-12712199	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	esv1812058	chr16:12680270-12712059	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv9351	chr16:12681377-12708042	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv1047005	chr16:12683657-12704840	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv1051014	chr16:12683657-12722792	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9922786	GRIN2A	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12681000-12686400	Enhancers	HepG2	liver
2	chr16:12683600-12685000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr16:12683600-12685400	Enhancers	GM12878-XiMat	blood
4	chr16:12684600-12685600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr16:12684600-12686400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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