Variant report

Variant	rs12236852
Chromosome Location	chr9:8956603-8956604
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10511515	0.96[CEU][hapmap]
rs10739179	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759021	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10816012	0.81[JPT][hapmap]
rs10816019	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10816020	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816021	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816022	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs10977393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10977396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10977397	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10977413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10977415	0.81[JPT][hapmap]
rs10977417	0.81[JPT][hapmap]
rs10977418	0.81[JPT][hapmap]
rs11788709	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1368676	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1368677	0.81[JPT][hapmap]
rs1368678	0.81[JPT][hapmap]
rs1368687	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap]
rs1433553	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs1594766	0.96[CEU][hapmap]
rs1897678	0.81[JPT][hapmap]
rs2381933	0.81[JPT][hapmap]
rs2890842	0.82[CEU][hapmap]
rs4314697	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4380999	1.00[CEU][hapmap]
rs4740970	0.81[JPT][hapmap]
rs4742552	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap]
rs4742553	0.85[CEU][hapmap]
rs4742554	1.00[CEU][hapmap]
rs7021685	0.95[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs7047447	0.81[JPT][hapmap]
rs72708121	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7852703	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs7856243	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs7863982	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS 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 miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer 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
3	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1015898	chr9:8753534-9011443	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2762789	chr9:8903357-9030039	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv613299	chr9:8903857-9032105	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1023691	chr9:8907952-9030627	Weak transcription Enhancers Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv539981	chr9:8907952-9030627	Enhancers Weak transcription Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv969748	chr9:8924798-8993842	Enhancers Weak transcription Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv892246	chr9:8926071-8993027	Weak transcription Enhancers Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1021214	chr9:8929663-9011443	Weak transcription Enhancers Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1015673	chr9:8929663-9016071	Enhancers Flanking Active TSS Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv466125	chr9:8939940-8993618	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
14	nsv466126	chr9:8939940-8993618	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
15	nsv613300	chr9:8939940-8993618	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8950000-8961200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:8955000-8957200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:8955200-8957000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr9:8955200-8957000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr9:8955400-8956800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:8956000-8956800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:8956200-8957200	Weak transcription	Brain Substantia Nigra	brain
8	chr9:8956600-8957200	Enhancers	Brain Cingulate Gyrus	brain

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