Variant report

Variant	rs10890405
Chromosome Location	chr1:47040084-47040085
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47027064..47029429-chr1:47037828..47041063,3	K562	blood:
2	chr1:47038566..47040285-chr1:47040736..47042855,2	K562	blood:
3	chr1:47038329..47041159-chr1:47076859..47079950,3	K562	blood:

Variant related genes	Relation type
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1054743	0.94[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs11211306	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211309	0.89[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs11211312	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211317	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211328	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12029680	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12047046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12048342	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12093643	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12138971	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1933934	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3753359	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766236	0.82[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766240	0.82[CEU][hapmap];0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs3818323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55680528	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56869893	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59446321	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6429606	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7552833	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7556307	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs764803	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8602	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs9659890	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804164	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9804165	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1009899	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv534954	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv1011892	chr1:47010519-47067492	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10890405	MKNK1	cis	Whole Blood	GTEx
rs10890405	MKNK1	cis	lung	GTEx
rs10890405	MKNK1	Cis_1M	lymphoblastoid	RTeQTL
rs10890405	MOB3C	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47015800-47041200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:47015800-47043400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:47019800-47043600	Weak transcription	Dnd41	blood
4	chr1:47020800-47047400	Weak transcription	Brain Germinal Matrix	brain
5	chr1:47021000-47057000	Weak transcription	Fetal Brain Male	brain
6	chr1:47021200-47045000	Weak transcription	K562	blood
7	chr1:47021800-47054600	Weak transcription	A549	lung
8	chr1:47022200-47043400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:47022400-47053600	Strong transcription	Thymus	Thymus
10	chr1:47022600-47051400	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:47022600-47051600	Strong transcription	Liver	Liver
12	chr1:47023000-47044200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr1:47023000-47047400	Strong transcription	Primary T cells from cord blood	blood
14	chr1:47023200-47044400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:47023200-47046600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:47023200-47047200	Strong transcription	Fetal Thymus	thymus
17	chr1:47023200-47051200	Strong transcription	Fetal Muscle Leg	muscle
18	chr1:47023200-47060000	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:47023400-47044600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:47023800-47045200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:47023800-47053200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:47024000-47054800	Weak transcription	HUVEC	blood vessel
23	chr1:47024600-47042400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:47025000-47041600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:47025600-47062400	Weak transcription	Fetal Heart	heart
26	chr1:47027000-47041000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:47027200-47047600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:47027600-47043400	Weak transcription	HepG2	liver
29	chr1:47028800-47041000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:47028800-47043600	Weak transcription	HMEC	breast
31	chr1:47028800-47044800	Weak transcription	Stomach Mucosa	stomach
32	chr1:47029000-47041800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:47029200-47042200	Weak transcription	NHLF	lung
34	chr1:47030800-47041000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:47030800-47046000	Weak transcription	Psoas Muscle	Psoas
36	chr1:47031000-47041800	Weak transcription	Brain Anterior Caudate	brain
37	chr1:47031200-47041000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:47031200-47045600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr1:47031400-47043400	Weak transcription	Osteobl	bone
40	chr1:47031600-47042000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:47031600-47042000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:47032600-47046200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr1:47033000-47041200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:47033200-47040400	Weak transcription	HSMM	muscle
45	chr1:47033200-47042000	Weak transcription	Small Intestine	intestine
46	chr1:47033200-47043000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:47033400-47041000	Weak transcription	Fetal Brain Female	brain
48	chr1:47033600-47042400	Weak transcription	Colonic Mucosa	Colon
49	chr1:47034200-47042000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:47034200-47044800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links