Variant report

Variant	rs383307
Chromosome Location	chr12:50277129-50277130
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50277027..50279310-chr12:50281448..50284241,3	K562	blood:
2	chr12:50277027..50279179-chr12:50280863..50283617,2	K562	blood:
3	chr12:50261251..50262807-chr12:50275153..50277323,2	MCF-7	breast:
4	chr12:50276293..50279154-chr12:50504715..50507254,2	MCF-7	breast:
5	chr12:50275514..50280639-chr12:50281373..50284133,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272368	Chromatin interaction
ENSG00000178449	Chromatin interaction

Extended variants
information (count: 17 )
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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1248264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423934	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[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	0.81[CHD][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs836959	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]
rs836967	0.81[CHD][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs836969	0.83[ASN][1000 genomes]
rs836970	0.82[ASN][1000 genomes]
rs897057	0.81[CHD][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
rs383307	C12orf62	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50267000-50297000	Weak transcription	Right Atrium	heart
2	chr12:50273600-50277800	Strong transcription	Brain Angular Gyrus	brain
3	chr12:50274600-50278800	Weak transcription	Fetal Kidney	kidney
4	chr12:50274800-50277600	Genic enhancers	Brain Inferior Temporal Lobe	brain
5	chr12:50275000-50294800	Weak transcription	Fetal Brain Male	brain
6	chr12:50275200-50279800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:50275200-50282000	Weak transcription	Gastric	stomach
8	chr12:50275400-50277200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:50275400-50277600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:50275400-50280200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:50275800-50277200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr12:50275800-50277400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr12:50275800-50277400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:50275800-50277600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr12:50276000-50277200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr12:50276000-50277400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr12:50276000-50277600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr12:50276000-50277600	Genic enhancers	Brain Cingulate Gyrus	brain
19	chr12:50276000-50277800	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr12:50276000-50277800	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr12:50276000-50277800	Enhancers	Brain Substantia Nigra	brain
22	chr12:50276000-50278200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:50276200-50277400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr12:50276200-50277600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:50276200-50277600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr12:50276400-50277200	Genic enhancers	Brain Hippocampus Middle	brain
27	chr12:50276400-50277200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:50276400-50278200	Weak transcription	Fetal Brain Female	brain
29	chr12:50276600-50279000	Weak transcription	Brain Germinal Matrix	brain
30	chr12:50276800-50277200	ZNF genes & repeats	Fetal Stomach	stomach
31	chr12:50276800-50277400	Enhancers	H9 Cell Line	embryonic stem cell
32	chr12:50276800-50277400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:50277000-50277200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:50277000-50277200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:50277000-50278200	Weak transcription	Hela-S3	cervix
36	chr12:50277000-50279000	Weak transcription	Brain Anterior Caudate	brain
37	chr12:50277000-50279600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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