Variant report

Variant	rs4660919
Chromosome Location	chr1:46754486-46754487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46752392..46755231-chr1:46809649..46812532,2	K562	blood:
2	chr1:46730224..46732084-chr1:46754046..46756082,3	K562	blood:
3	chr1:46712253..46715558-chr1:46749979..46754633,4	K562	blood:
4	chr1:46753129..46754976-chr1:46756242..46758158,2	MCF-7	breast:
5	chr1:46753268..46755813-chr1:46767246..46769063,2	MCF-7	breast:
6	chr1:46750679..46754864-chr1:46805103..46809181,6	K562	blood:

Variant related genes	Relation type
ENSG00000085999	Chromatin interaction
ENSG00000132128	Chromatin interaction
ENSG00000117481	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10489770	0.82[MEX][hapmap]
rs10789488	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10890386	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10890387	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10890388	0.92[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11584233	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11586229	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12028248	0.82[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs12039667	0.82[AMR][1000 genomes]
rs12044708	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12125573	1.00[ASW][hapmap];0.95[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];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126187	1.00[MEX][hapmap]
rs12141269	1.00[MEX][hapmap]
rs12141928	0.94[MEX][hapmap]
rs1547180	0.82[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17102087	0.94[JPT][hapmap]
rs2093044	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4660918	0.92[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4660920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6429596	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6689182	0.91[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs6692775	0.82[CEU][hapmap];0.82[GIH][hapmap]
rs6696085	1.00[MEX][hapmap]
rs7527133	0.87[AMR][1000 genomes]
rs953070	0.82[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap]
rs9793263	0.88[ASW][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4660919	NSUN4	cis	parietal	SCAN
rs4660919	MMACHC	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46715200-46764200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:46715400-46763800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:46715400-46764400	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:46715400-46765600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:46720800-46766400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:46723200-46755200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:46724200-46756000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:46730000-46764000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:46733600-46766200	Weak transcription	Small Intestine	intestine
10	chr1:46741200-46755000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:46741600-46763400	Strong transcription	Fetal Stomach	stomach
12	chr1:46742600-46756000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr1:46742800-46756200	Strong transcription	Placenta	Placenta
14	chr1:46743200-46756000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr1:46743200-46756200	Strong transcription	Stomach Smooth Muscle	stomach
16	chr1:46743200-46763600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:46743400-46756000	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr1:46743400-46764000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:46743400-46764000	Strong transcription	Liver	Liver
20	chr1:46743600-46763800	Strong transcription	Fetal Lung	lung
21	chr1:46744600-46761400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:46745200-46766400	Weak transcription	Stomach Mucosa	stomach
23	chr1:46748800-46756000	Strong transcription	Adipose Nuclei	Adipose
24	chr1:46748800-46756000	Strong transcription	Brain Cingulate Gyrus	brain
25	chr1:46749000-46755000	Strong transcription	Brain Anterior Caudate	brain
26	chr1:46749400-46756400	Strong transcription	Fetal Brain Female	brain
27	chr1:46749600-46755000	Genic enhancers	K562	blood
28	chr1:46749600-46755800	Strong transcription	Brain Angular Gyrus	brain
29	chr1:46749800-46756000	Strong transcription	Brain Hippocampus Middle	brain
30	chr1:46749800-46756200	Strong transcription	HepG2	liver
31	chr1:46750400-46754800	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr1:46750600-46754600	Strong transcription	Ovary	ovary
33	chr1:46750600-46756400	Strong transcription	Fetal Intestine Large	intestine
34	chr1:46750600-46762400	Weak transcription	Fetal Brain Male	brain
35	chr1:46750800-46764200	Weak transcription	Right Atrium	heart
36	chr1:46751000-46756000	Strong transcription	Left Ventricle	heart
37	chr1:46751400-46760800	Weak transcription	Psoas Muscle	Psoas
38	chr1:46751400-46766200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:46751800-46759000	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:46751800-46759800	Weak transcription	Brain Substantia Nigra	brain
41	chr1:46751800-46762600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:46752000-46759800	Weak transcription	Pancreas	Pancrea
43	chr1:46752000-46760600	Weak transcription	Colonic Mucosa	Colon
44	chr1:46752000-46761000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:46752000-46761000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:46752000-46761200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:46752000-46762400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:46752000-46763000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:46752000-46765000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:46752200-46754600	Weak transcription	Rectal Smooth Muscle	rectum

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