Variant report

Variant	rs1547858
Chromosome Location	chr18:12366610-12366611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12362548..12366829-chr18:12375336..12378234,6	MCF-7	breast:
2	chr18:12308687..12311598-chr18:12366284..12368476,2	K562	blood:
3	chr18:12360702..12363372-chr18:12365362..12368276,3	MCF-7	breast:
4	chr18:12361542..12363556-chr18:12365660..12367206,2	K562	blood:
5	chr18:12308206..12311598-chr18:12363636..12368476,4	K562	blood:

Variant related genes	Relation type
ENSG00000141385	Chromatin interaction
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10853225	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11080571	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11080572	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11553521	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11662523	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11664216	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11875938	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12455273	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12604732	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12954686	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12968089	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12968566	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1941222	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003881	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2298542	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2298543	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2509510	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28372882	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35968035	0.91[ASN][1000 genomes]
rs3786260	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478088	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4797677	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4797680	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553091	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs566960	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs693449	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7231182	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7231409	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7235237	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7235296	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7407640	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8097342	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9303769	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9303771	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9635829	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9956171	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9960103	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9964406	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer 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	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv1060728	chr18:12364077-12410409	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1547858	TUBB6	Cis_1M	lymphoblastoid	RTeQTL
rs1547858	TUBB6	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12333200-12370800	Strong transcription	Fetal Muscle Trunk	muscle
2	chr18:12333200-12371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr18:12333400-12370200	Strong transcription	Fetal Thymus	thymus
4	chr18:12333400-12370800	Strong transcription	Fetal Muscle Leg	muscle
5	chr18:12333400-12371400	Strong transcription	Fetal Stomach	stomach
6	chr18:12333600-12369600	Strong transcription	Placenta	Placenta
7	chr18:12333600-12369800	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr18:12333800-12369400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr18:12334000-12369400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr18:12337000-12367600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr18:12337000-12374200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr18:12337200-12369400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr18:12337400-12369800	Strong transcription	Liver	Liver
14	chr18:12337400-12370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr18:12337800-12369600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr18:12337800-12370800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:12339200-12368800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:12339800-12370200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr18:12339800-12371400	Strong transcription	Dnd41	blood
20	chr18:12340000-12369400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr18:12340000-12369400	Strong transcription	HepG2	liver
22	chr18:12340000-12369600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr18:12340000-12370800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr18:12340000-12371400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr18:12340000-12371600	Strong transcription	GM12878-XiMat	blood
26	chr18:12340200-12369400	Strong transcription	Hela-S3	cervix
27	chr18:12340400-12367400	Strong transcription	Thymus	Thymus
28	chr18:12341000-12370800	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr18:12341000-12370800	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr18:12341000-12370800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr18:12341600-12369400	Strong transcription	Lung	lung
32	chr18:12341600-12370800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr18:12341800-12369400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr18:12349200-12369400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr18:12350600-12369600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr18:12353600-12369600	Strong transcription	Primary B cells from cord blood	blood
37	chr18:12354200-12369400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr18:12355200-12367600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr18:12355400-12367800	Strong transcription	HMEC	breast
40	chr18:12355400-12369400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr18:12356800-12369000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr18:12357800-12367800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr18:12357800-12369400	Strong transcription	Primary T cells from cord blood	blood
44	chr18:12357800-12369400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr18:12357800-12369600	Strong transcription	Esophagus	oesophagus
46	chr18:12358000-12372400	Strong transcription	NHEK	skin
47	chr18:12358200-12369400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr18:12358200-12369600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr18:12358600-12371400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr18:12359200-12370800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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