Variant report

Variant	rs12695695
Chromosome Location	chr3:139066649-139066650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:139066345-139066674	HepG2	liver:	n/a	chr3:139066541-139066552
2	POLR2A	chr3:139065642-139069144	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:139066217..139069193-chr3:139069576..139072044,3	MCF-7	breast:
2	chr3:139061660..139066893-chr3:139105523..139110764,11	K562	blood:
3	chr3:139063205..139066777-chr3:139105523..139110764,7	K562	blood:

Variant related genes	Relation type
MRPS22	TF binding region
ENSG00000175110	Chromatin interaction
ENSG00000248932	Chromatin interaction
ENSG00000252245	Chromatin interaction
ENSG00000184432	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13325144	0.84[EUR][1000 genomes]
rs34654084	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9821204	1.00[ASW][hapmap]
rs9839834	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9874641	1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.80[AMR][1000 genomes]
rs9878661	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005158	chr3:139001736-139073011	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv4034	chr3:139034976-139080133	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12695695	BPESC1	cis	cerebellum	SCAN
rs12695695	PAQR9	cis	cerebellum	SCAN
rs12695695	ATP1B3	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139063800-139070000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:139064000-139067000	Weak transcription	Fetal Kidney	kidney
3	chr3:139064000-139070200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:139064000-139073400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:139064000-139073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:139064000-139073600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:139064200-139067200	Weak transcription	NHLF	lung
8	chr3:139064200-139068200	Weak transcription	Stomach Mucosa	stomach
9	chr3:139064200-139068200	Weak transcription	A549	lung
10	chr3:139064200-139072600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:139064200-139089200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:139064400-139097200	Strong transcription	Fetal Muscle Leg	muscle
13	chr3:139064600-139067000	Weak transcription	Ovary	ovary
14	chr3:139064600-139069600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:139064800-139068000	Weak transcription	NHDF-Ad	bronchial
16	chr3:139064800-139068600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:139064800-139068800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:139064800-139071200	Weak transcription	Fetal Heart	heart
19	chr3:139064800-139074800	Weak transcription	Right Atrium	heart
20	chr3:139064800-139094600	Strong transcription	Primary B cells from cord blood	blood
21	chr3:139065000-139067600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:139065000-139096200	Strong transcription	Fetal Intestine Large	intestine
23	chr3:139065000-139101200	Strong transcription	Primary T cells from cord blood	blood
24	chr3:139065000-139103800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:139065000-139103800	Strong transcription	HSMM	muscle
26	chr3:139065000-139104000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:139065200-139066800	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:139065200-139069000	Weak transcription	Small Intestine	intestine
29	chr3:139065200-139073200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:139065200-139073200	Strong transcription	K562	blood
31	chr3:139065200-139089200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:139065200-139093600	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:139065200-139096800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:139065200-139098000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:139065200-139102000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:139065200-139102200	Strong transcription	Fetal Muscle Trunk	muscle
37	chr3:139065400-139067200	Strong transcription	Brain Hippocampus Middle	brain
38	chr3:139065400-139067600	Strong transcription	Hela-S3	cervix
39	chr3:139065400-139068400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:139065400-139073800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:139065400-139077000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:139065400-139077600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:139065400-139097600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:139065400-139102200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:139065400-139102400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr3:139065400-139102600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:139065400-139102600	Strong transcription	Osteobl	bone
48	chr3:139065400-139103600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:139065400-139103800	Strong transcription	Fetal Thymus	thymus
50	chr3:139065600-139067400	Strong transcription	Brain Inferior Temporal Lobe	brain

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