Variant report

Variant	rs10500372
Chromosome Location	chr16:10125046-10125047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:10125039..10125982-chr16:10274667..10276015,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183454	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10500370	0.87[ASW][hapmap];0.83[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10500371	0.83[CEU][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10500373	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11642357	0.90[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs1213316	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12447252	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12598055	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12598112	0.88[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12599024	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17682922	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17682940	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17750208	0.87[ASW][hapmap];0.83[CEU][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes]
rs17750303	0.87[ASW][hapmap];0.83[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650424	0.81[EUR][1000 genomes]
rs2650427	0.91[JPT][hapmap]
rs3859123	0.82[CHD][hapmap]
rs3859125	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs3859126	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4363863	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs837691	0.80[CHB][hapmap]
rs837692	0.85[JPT][hapmap]
rs837694	0.91[JPT][hapmap]
rs837707	0.91[JPT][hapmap]
rs865678	0.85[JPT][hapmap]
rs9788936	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9788939	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9921906	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949196	chr16:9937980-10182349	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1037001	chr16:10008023-10476482	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422500	chr16:10008309-10415517	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1052566	chr16:10033178-10260068	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2758410	chr16:10060976-10257550	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2758629	chr16:10060976-10257550	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv427973	chr16:10060976-10257550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1037707	chr16:10078790-10529893	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1042727	chr16:10092002-10521096	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv932624	chr16:10092048-10520294	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1045651	chr16:10106137-10520295	Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv542742	chr16:10106137-10520295	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1053991	chr16:10106137-10532500	Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv542743	chr16:10106137-10532500	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv533421	chr16:10106138-10520294	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1036532	chr16:10107173-10520100	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv542744	chr16:10107173-10520100	Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv1050509	chr16:10107173-10564913	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv542745	chr16:10107173-10564913	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv1050835	chr16:10110040-10128164	Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv571443	chr16:10112199-10184183	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10500372	GRIN2A	cis	parietal	SCAN
rs10500372	PRM1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:10124400-10125600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
2	chr16:10124400-10127400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr16:10124400-10131800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:10124800-10127200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr16:10124800-10127400	Weak transcription	Brain Angular Gyrus	brain

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