Variant report

Variant	rs12118770
Chromosome Location	chr1:154397589-154397590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154296724..154297553-chr1:154396976..154397711,2	MCF-7	breast:
2	chr1:154395281..154397950-chr1:154401613..154403771,2	K562	blood:
3	chr1:154396249..154398613-chr1:154405064..154407667,2	MCF-7	breast:
4	chr1:154389348..154391422-chr1:154394906..154397857,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10908837	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10908838	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265611	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265612	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12117832	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118721	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12129500	0.81[AMR][1000 genomes]
rs4553185	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845371	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845618	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845619	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845625	0.87[AMR][1000 genomes]
rs59632925	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427658	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6667434	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6683206	0.80[EUR][1000 genomes]
rs6686750	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6687726	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689306	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6689393	0.87[AMR][1000 genomes]
rs6694258	0.87[AMR][1000 genomes]
rs6694817	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526131	0.81[AMR][1000 genomes]
rs7536152	0.81[AMR][1000 genomes]
rs7549250	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7549338	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7553796	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12118770	TDRD10	cis	lung	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154383000-154402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154389000-154402800	Enhancers	Stomach Mucosa	stomach
3	chr1:154390800-154398000	Enhancers	Placenta	Placenta
4	chr1:154391600-154399600	Weak transcription	Brain Germinal Matrix	brain
5	chr1:154392800-154398000	Enhancers	Duodenum Mucosa	Duodenum
6	chr1:154392800-154398800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:154392800-154399600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:154392800-154400200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr1:154392800-154400600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:154392800-154402800	Weak transcription	Fetal Brain Male	brain
11	chr1:154393000-154405800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr1:154393600-154402800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:154393800-154399800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:154393800-154401200	Enhancers	Hela-S3	cervix
15	chr1:154393800-154402600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:154393800-154403600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:154394000-154404000	Weak transcription	GM12878-XiMat	blood
18	chr1:154394200-154398000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:154394200-154399800	Weak transcription	Ovary	ovary
20	chr1:154395000-154397800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:154395200-154398000	Enhancers	HepG2	liver
22	chr1:154395600-154398000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:154395600-154400200	Weak transcription	Fetal Thymus	thymus
24	chr1:154395600-154401200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:154396600-154398200	Genic enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:154396800-154397800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:154396800-154398000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:154396800-154398000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr1:154396800-154398400	Genic enhancers	Monocytes-CD14+_RO01746	blood
30	chr1:154396800-154399800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:154396800-154399800	Enhancers	Colon Smooth Muscle	Colon
32	chr1:154396800-154400000	Weak transcription	Fetal Brain Female	brain
33	chr1:154396800-154401200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:154396800-154401600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:154396800-154402200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:154397000-154397600	Enhancers	Stomach Smooth Muscle	stomach
37	chr1:154397000-154397800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:154397000-154398000	Weak transcription	Psoas Muscle	Psoas
39	chr1:154397000-154399200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:154397000-154399600	Weak transcription	Colonic Mucosa	Colon
41	chr1:154397000-154399600	Weak transcription	Esophagus	oesophagus
42	chr1:154397000-154399800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:154397000-154399800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:154397000-154399800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:154397000-154399800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:154397000-154399800	Weak transcription	Fetal Lung	lung
47	chr1:154397000-154399800	Weak transcription	Fetal Stomach	stomach
48	chr1:154397000-154399800	Weak transcription	Spleen	Spleen
49	chr1:154397000-154399800	Weak transcription	HSMMtube	muscle
50	chr1:154397000-154400000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links