Variant report

Variant	rs12486445
Chromosome Location	chr3:157886699-157886700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:157863466..157866461-chr3:157886047..157887794,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10513526	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs12487397	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs12487873	0.86[CEU][hapmap];0.88[JPT][hapmap]
rs12490116	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12495621	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17683721	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17683787	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2176890	0.81[EUR][1000 genomes]
rs2362247	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4542974	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs55638807	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61244743	0.83[EUR][1000 genomes]
rs73164073	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73164083	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73164088	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73164089	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73164094	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166303	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166305	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73166307	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166311	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166326	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73166328	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73166334	0.83[EUR][1000 genomes]
rs73166338	0.83[EUR][1000 genomes]
rs73166343	0.83[EUR][1000 genomes]
rs7650062	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]

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	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12486445	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157843600-157886800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:157846200-157893400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:157846200-157893600	Weak transcription	Aorta	Aorta
4	chr3:157846800-157894400	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:157848000-157888200	Weak transcription	Thymus	Thymus
6	chr3:157848200-157886800	Weak transcription	Ovary	ovary
7	chr3:157849400-157894400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:157854600-157911800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:157856200-157894400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr3:157856400-157892400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:157860800-157886800	Weak transcription	Left Ventricle	heart
12	chr3:157868200-157916200	Weak transcription	Primary B cells from cord blood	blood
13	chr3:157869400-157887600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:157873200-157902000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:157874000-157889600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:157879200-157896000	Weak transcription	Pancreas	Pancrea
17	chr3:157882800-157886800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:157883000-157887200	Enhancers	NHDF-Ad	bronchial
19	chr3:157883200-157887800	Enhancers	Hela-S3	cervix
20	chr3:157883200-157887800	Enhancers	Osteobl	bone
21	chr3:157883400-157887200	Enhancers	HUVEC	blood vessel
22	chr3:157883400-157887800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:157884400-157894800	Weak transcription	Fetal Thymus	thymus
24	chr3:157884800-157887200	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:157885000-157889000	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:157885200-157887400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:157885200-157887400	Enhancers	HSMM	muscle
28	chr3:157885200-157887600	Enhancers	HSMMtube	muscle
29	chr3:157885200-157887600	Enhancers	NH-A	brain
30	chr3:157885200-157889600	Weak transcription	Psoas Muscle	Psoas
31	chr3:157885400-157887000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr3:157885400-157887200	Enhancers	NHEK	skin
33	chr3:157885400-157887600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:157885400-157887600	Enhancers	HMEC	breast
35	chr3:157885400-157887800	Enhancers	Muscle Satellite Cultured Cells	--
36	chr3:157885400-157889000	Enhancers	Stomach Mucosa	stomach
37	chr3:157885600-157886800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:157885600-157886800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:157885600-157887000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:157885600-157887000	Enhancers	Primary hematopoietic stem cells	blood
41	chr3:157885600-157887000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:157885600-157887000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:157885600-157887000	Enhancers	NHLF	lung
44	chr3:157885600-157887400	Strong transcription	Primary T cells from cord blood	blood
45	chr3:157885600-157887400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:157885800-157887000	Weak transcription	Gastric	stomach
47	chr3:157886000-157887000	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr3:157886000-157887200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:157886000-157887600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:157886000-157887600	Enhancers	K562	blood

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