Variant report

Variant	rs12146051
Chromosome Location	chr1:46742952-46742953
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46711512..46718649-chr1:46736779..46744030,9	K562	blood:
2	chr1:46742647..46744307-chr1:46779144..46781501,2	K562	blood:
3	chr1:46712196..46714298-chr1:46742242..46744030,2	K562	blood:
4	chr1:46737844..46741686-chr1:46742453..46744741,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085999	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12137934	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361819	0.80[CEU][hapmap]
rs17361887	1.00[CHB][hapmap]
rs2019996	0.83[EUR][1000 genomes]
rs55707872	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658556	1.00[CHB][hapmap]
rs6662982	1.00[CHB][hapmap]
rs6696284	1.00[CHB][hapmap]
rs6697623	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533750	1.00[CHB][hapmap]
rs7555458	1.00[CHB][hapmap]
rs9429187	1.00[CHB][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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS 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 miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12146051	NSUN4	cis	multi-tissue	Pritchard
rs12146051	NSUN4	cis	Whole Blood	GTEx
rs12146051	hmm8232	cis	multi-tissue	Pritchard
rs12146051	NSUN4	Cis_1M	lymphoblastoid	RTeQTL
rs12146051	FAAH	cis	Whole Blood	GTEx
rs12146051	NSUN4	cis	Muscle Skeletal	GTEx
rs12146051	FAAH	cis	Esophagus Mucosa	GTEx
rs12146051	FAAH	cis	Esophagus Muscularis	GTEx
rs12146051	RP5-1109J22.1	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46713600-46743600	Weak transcription	Aorta	Aorta
2	chr1:46713800-46743400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:46714200-46743200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:46714200-46743400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:46714200-46743400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:46714200-46743600	Weak transcription	Gastric	stomach
7	chr1:46714200-46743800	Weak transcription	Right Atrium	heart
8	chr1:46714400-46743400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:46714400-46745400	Weak transcription	Fetal Brain Male	brain
10	chr1:46714400-46745600	Weak transcription	Fetal Kidney	kidney
11	chr1:46714400-46754200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:46714600-46748600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:46714600-46749600	Weak transcription	Fetal Heart	heart
14	chr1:46714800-46748400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:46715000-46752800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:46715200-46743400	Weak transcription	Spleen	Spleen
17	chr1:46715200-46748000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr1:46715200-46748400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:46715200-46764200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:46715400-46748200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:46715400-46748400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:46715400-46748400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:46715400-46753000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:46715400-46754200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:46715400-46763800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:46715400-46764400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:46715400-46765600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:46716000-46749400	Strong transcription	Fetal Thymus	thymus
29	chr1:46717200-46748000	Strong transcription	Thymus	Thymus
30	chr1:46718200-46749600	Strong transcription	Dnd41	blood
31	chr1:46719800-46743200	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:46720600-46750800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:46720800-46766400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:46721400-46745000	Strong transcription	HepG2	liver
35	chr1:46721600-46753800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:46721800-46743000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:46721800-46744200	Weak transcription	Primary T cells from cord blood	blood
38	chr1:46721800-46750600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:46723000-46743400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:46723200-46743400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:46723200-46743400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:46723200-46743400	Weak transcription	Brain Substantia Nigra	brain
43	chr1:46723200-46747000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr1:46723200-46755200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:46724200-46756000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:46724800-46743200	Weak transcription	Right Ventricle	heart
47	chr1:46725400-46748000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:46726200-46747800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:46726400-46743400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:46726600-46743200	Weak transcription	Stomach Smooth Muscle	stomach

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