Variant report

Variant	rs9960103
Chromosome Location	chr18:12372214-12372215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12360642..12363502-chr18:12370085..12373310,4	K562	blood:
2	chr18:12274350..12275873-chr18:12371406..12373710,2	K562	blood:
3	chr18:12330814..12333752-chr18:12371346..12373010,2	MCF-7	breast:
4	chr18:12369983..12374854-chr18:12375235..12379102,8	MCF-7	breast:
5	chr18:12342599..12345334-chr18:12370833..12373384,2	K562	blood:
6	chr18:12283750..12286656-chr18:12370266..12373091,2	K562	blood:

Variant related genes	Relation type
ENSG00000141385	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	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11080571	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11080572	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11553521	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11662523	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11664216	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11875938	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12455273	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12604732	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12954686	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12968089	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12968566	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1547858	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941222	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003881	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2298542	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2298543	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2509510	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28372882	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35968035	0.91[ASN][1000 genomes]
rs3786260	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478088	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4797677	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4797680	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553091	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs566960	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs693449	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7231182	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7231409	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7235237	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7235296	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7407640	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8097342	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9303769	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9303771	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9635829	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9956171	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9964406	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[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
rs9960103	TUBB6	Cis_1M	lymphoblastoid	RTeQTL
rs9960103	TUBB6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12337000-12374200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:12358000-12372400	Strong transcription	NHEK	skin
3	chr18:12359200-12376000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr18:12359800-12375800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr18:12360000-12373400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr18:12367600-12372400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr18:12367600-12372600	Weak transcription	NHDF-Ad	bronchial
8	chr18:12367600-12373200	Weak transcription	HSMM	muscle
9	chr18:12367600-12376000	Weak transcription	Fetal Kidney	kidney
10	chr18:12367800-12372400	Weak transcription	Brain Hippocampus Middle	brain
11	chr18:12367800-12372800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr18:12367800-12373400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr18:12367800-12374400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr18:12367800-12375400	Weak transcription	HMEC	breast
15	chr18:12368600-12372400	Weak transcription	HSMMtube	muscle
16	chr18:12368600-12373000	Weak transcription	HUVEC	blood vessel
17	chr18:12368800-12374400	Weak transcription	Fetal Brain Male	brain
18	chr18:12368800-12375400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr18:12369000-12372400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr18:12369200-12372600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr18:12369400-12372400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr18:12369400-12372400	Weak transcription	Brain Angular Gyrus	brain
23	chr18:12369400-12372400	Weak transcription	Brain Anterior Caudate	brain
24	chr18:12369400-12372400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr18:12369400-12372400	Weak transcription	Psoas Muscle	Psoas
26	chr18:12369400-12372400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr18:12369400-12372400	Weak transcription	NH-A	brain
28	chr18:12369400-12372600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr18:12369400-12372600	Weak transcription	Colon Smooth Muscle	Colon
30	chr18:12369400-12372600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr18:12369400-12372600	Weak transcription	Hela-S3	cervix
32	chr18:12369400-12372800	Weak transcription	Fetal Brain Female	brain
33	chr18:12369400-12372800	Weak transcription	HepG2	liver
34	chr18:12369400-12373000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr18:12369400-12373000	Weak transcription	Brain Germinal Matrix	brain
36	chr18:12369400-12373200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr18:12369400-12373200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr18:12369400-12373200	Weak transcription	Aorta	Aorta
39	chr18:12369400-12373600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr18:12369400-12373600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr18:12369400-12373600	Weak transcription	Lung	lung
42	chr18:12369400-12373600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr18:12369400-12374000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr18:12369400-12374200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr18:12369400-12374600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr18:12369400-12374600	Weak transcription	Adipose Nuclei	Adipose
47	chr18:12369400-12374600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr18:12369400-12375000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr18:12369400-12375000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr18:12369400-12375400	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links