Variant report

Variant	rs836959
Chromosome Location	chr12:50275137-50275138
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50273812..50276593-chr12:50279241..50281059,2	K562	blood:
2	chr12:50275093..50276632-chr12:50278592..50280741,2	K562	blood:
3	chr12:50269088..50271373-chr12:50274652..50276581,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1248263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1248264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423934	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs447016	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs706797	0.83[ASN][1000 genomes]
rs706798	0.83[CHD][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs836967	0.83[CHD][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs836969	0.83[ASN][1000 genomes]
rs836970	0.82[ASN][1000 genomes]
rs897057	0.84[CHD][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv3372497	chr12:50269585-50276583	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3401982	chr12:50270085-50275683	Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3380248	chr12:50270185-50275783	Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3378768	chr12:50270385-50275883	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs836959	C12orf62	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50266200-50275400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:50267000-50275800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:50267000-50297000	Weak transcription	Right Atrium	heart
4	chr12:50268200-50276400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:50269400-50275400	Weak transcription	Fetal Stomach	stomach
6	chr12:50270000-50276400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:50273000-50276400	Strong transcription	Fetal Brain Female	brain
8	chr12:50273600-50277800	Strong transcription	Brain Angular Gyrus	brain
9	chr12:50274400-50275400	Strong transcription	Brain Germinal Matrix	brain
10	chr12:50274600-50275200	Weak transcription	Fetal Lung	lung
11	chr12:50274600-50275200	Enhancers	Fetal Muscle Trunk	muscle
12	chr12:50274600-50275600	Enhancers	Fetal Muscle Leg	muscle
13	chr12:50274600-50275800	Weak transcription	Brain Anterior Caudate	brain
14	chr12:50274600-50276000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:50274600-50278800	Weak transcription	Fetal Kidney	kidney
16	chr12:50274800-50275600	Enhancers	Placenta	Placenta
17	chr12:50274800-50276000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:50274800-50276000	Weak transcription	Brain Substantia Nigra	brain
19	chr12:50274800-50276400	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:50274800-50277600	Genic enhancers	Brain Inferior Temporal Lobe	brain
21	chr12:50275000-50275200	Enhancers	Gastric	stomach
22	chr12:50275000-50275400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:50275000-50294800	Weak transcription	Fetal Brain Male	brain

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