Variant report

Variant	rs12245875
Chromosome Location	chr10:3856293-3856294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:3856210..3857914-chr10:3861188..3862923,2	K562	blood:
2	chr10:3835603..3838391-chr10:3855439..3857235,2	MCF-7	breast:
3	chr10:3852665..3856843-chr10:3893810..3896491,3	K562	blood:
4	chr10:3854297..3857056-chr10:3857370..3862242,4	MCF-7	breast:
5	chr10:3822110..3831216-chr10:3843525..3857606,41	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067082	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10508268	0.82[CEU][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11252113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12248147	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12268277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761012	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34180227	0.89[EUR][1000 genomes]
rs34414469	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61829733	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61829734	0.88[AMR][1000 genomes];0.98[EUR][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	nsv1043680	chr10:3551191-4038002	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv540450	chr10:3804336-3859639	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv540451	chr10:3804336-3868002	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv540456	chr10:3820854-3868002	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	n/a
5	nsv1045571	chr10:3839308-3874184	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	nsv540458	chr10:3839308-3874184	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12245875	PFKP	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:3851400-3856800	Enhancers	Fetal Heart	heart
2	chr10:3853800-3856400	Enhancers	A549	lung
3	chr10:3853800-3856800	Enhancers	HepG2	liver
4	chr10:3854000-3856800	Enhancers	HSMM	muscle
5	chr10:3854000-3857400	Weak transcription	Thymus	Thymus
6	chr10:3854200-3856800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr10:3854400-3856400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr10:3854400-3859000	Weak transcription	K562	blood
9	chr10:3854400-3861800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr10:3854600-3856400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:3854600-3856400	Weak transcription	Fetal Thymus	thymus
12	chr10:3854600-3856800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr10:3854600-3858800	Enhancers	Dnd41	blood
14	chr10:3854600-3859200	Weak transcription	Left Ventricle	heart
15	chr10:3854600-3862000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:3854600-3867800	Weak transcription	NHLF	lung
17	chr10:3854800-3857400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr10:3855000-3857200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr10:3855000-3857400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr10:3855200-3856600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:3855200-3856600	Enhancers	HMEC	breast
22	chr10:3855400-3856600	Enhancers	NH-A	brain
23	chr10:3855400-3856800	Enhancers	NHDF-Ad	bronchial
24	chr10:3855400-3856800	Enhancers	Osteobl	bone
25	chr10:3855800-3856400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr10:3855800-3856600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr10:3855800-3856600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:3855800-3856800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:3855800-3856800	Enhancers	HSMMtube	muscle
30	chr10:3855800-3857200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr10:3855800-3857600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr10:3856000-3856400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr10:3856000-3856800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr10:3856200-3856400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr10:3856200-3856400	Enhancers	Adipose Nuclei	Adipose
36	chr10:3856200-3856400	Enhancers	NHEK	skin
37	chr10:3856200-3856600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr10:3856200-3867400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links