Variant report

Variant	rs12426679
Chromosome Location	chr12:76237987-76237988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76234777..76238439-chr12:76239479..76242748,4	MCF-7	breast:
2	chr12:76230979..76233331-chr12:76235384..76238133,2	MCF-7	breast:
3	chr12:76237386..76239168-chr12:76425200..76427643,2	MCF-7	breast:
4	chr12:76231188..76233344-chr12:76237057..76238721,2	K562	blood:
5	chr12:76231844..76233597-chr12:76237057..76239947,2	K562	blood:

Variant related genes	Relation type
ENSG00000139289	Chromatin interaction
ENSG00000257839	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10879992	0.88[EUR][1000 genomes]
rs10879993	0.88[EUR][1000 genomes]
rs11180703	0.83[AMR][1000 genomes]
rs11180710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[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]
rs11180711	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11180712	0.88[EUR][1000 genomes]
rs11180713	0.88[EUR][1000 genomes]
rs11180714	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs11180719	0.85[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs12227868	0.85[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs12229980	0.88[EUR][1000 genomes]
rs12230172	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs12423455	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12426691	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463754	0.88[EUR][1000 genomes]
rs1493791	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs1493792	0.88[EUR][1000 genomes]
rs1493793	0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1493794	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs1493795	0.88[EUR][1000 genomes]
rs1532293	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1565765	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34439598	0.88[EUR][1000 genomes]
rs35080799	0.88[EUR][1000 genomes]
rs56044716	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61925073	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv832463	chr12:76136551-76316703	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv899315	chr12:76163309-76385096	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1041730	chr12:76198863-76331900	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12426679	BBS10	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76228600-76239800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:76228600-76250000	Weak transcription	Pancreas	Pancrea
3	chr12:76232200-76241400	Weak transcription	Fetal Stomach	stomach
4	chr12:76235600-76242600	Weak transcription	Left Ventricle	heart
5	chr12:76236000-76238400	Weak transcription	HUVEC	blood vessel
6	chr12:76236000-76239000	Weak transcription	Brain Angular Gyrus	brain
7	chr12:76236000-76239400	Weak transcription	Fetal Brain Female	brain
8	chr12:76236000-76242000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:76236200-76238000	Weak transcription	Fetal Lung	lung
10	chr12:76236200-76238800	Weak transcription	Brain Anterior Caudate	brain
11	chr12:76236200-76239000	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:76236400-76239000	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:76236400-76239000	Weak transcription	Brain Substantia Nigra	brain
14	chr12:76236400-76239200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:76236400-76242000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:76236600-76239000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:76236800-76241200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:76236800-76241400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:76237200-76238200	Weak transcription	Brain Germinal Matrix	brain
20	chr12:76237400-76238400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:76237400-76239200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:76237600-76238800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:76237800-76238000	Enhancers	Fetal Brain Male	brain
24	chr12:76237800-76238000	Weak transcription	K562	blood
25	chr12:76237800-76239600	Enhancers	HepG2	liver

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