Variant report

Variant	rs73239111
Chromosome Location	chr3:113145710-113145711
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIDT1-1	chr3:113145564-113145893	ENSG00000243849.1

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10934229	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10934230	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10934231	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11923005	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12233528	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12630518	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12635786	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12636607	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12636959	0.80[EUR][1000 genomes]
rs12637924	0.86[EUR][1000 genomes]
rs16860850	0.81[EUR][1000 genomes]
rs16860868	0.81[EUR][1000 genomes]
rs16860899	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2291413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3732806	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4682136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682137	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682485	0.81[EUR][1000 genomes]
rs55667700	0.81[EUR][1000 genomes]
rs55710804	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55748551	0.81[EUR][1000 genomes]
rs55757335	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56339567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60329418	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62265992	0.81[EUR][1000 genomes]
rs6779002	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6779305	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73235059	0.80[EUR][1000 genomes]
rs73235065	0.81[EUR][1000 genomes]
rs73237104	0.86[EUR][1000 genomes]
rs73237110	0.86[EUR][1000 genomes]
rs73237123	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73237130	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73237136	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73237142	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73237143	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73237146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73239107	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73239117	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73239120	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73239121	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73239126	0.86[EUR][1000 genomes]
rs7625933	0.83[AMR][1000 genomes]
rs763805	0.80[EUR][1000 genomes]
rs8179926	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers 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 miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113102200-113148800	Weak transcription	Brain Angular Gyrus	brain
3	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:113111600-113146400	Weak transcription	Brain Substantia Nigra	brain
5	chr3:113112200-113148400	Weak transcription	Brain Anterior Caudate	brain
6	chr3:113117600-113148400	Weak transcription	Placenta	Placenta
7	chr3:113132600-113146400	Weak transcription	Right Ventricle	heart
8	chr3:113133200-113147800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:113134600-113159800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:113135200-113164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:113136000-113176400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:113137400-113148600	Weak transcription	Small Intestine	intestine
13	chr3:113137400-113160000	Weak transcription	Fetal Stomach	stomach
14	chr3:113140000-113160000	Weak transcription	Psoas Muscle	Psoas
15	chr3:113141400-113147800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:113143000-113147400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:113143200-113146000	ZNF genes & repeats	GM12878-XiMat	blood
18	chr3:113143200-113146800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:113143400-113146200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:113143400-113146600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:113143400-113147200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr3:113143400-113147200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:113143400-113147600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:113143600-113146000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr3:113143600-113146000	Strong transcription	Fetal Intestine Large	intestine
26	chr3:113143600-113146200	ZNF genes & repeats	Primary B cells from cord blood	blood
27	chr3:113143600-113146400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr3:113143600-113146800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr3:113143600-113147200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:113143600-113148000	Strong transcription	Left Ventricle	heart
31	chr3:113143800-113145800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:113143800-113145800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:113143800-113146000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:113143800-113146000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:113143800-113146000	Strong transcription	Fetal Thymus	thymus
36	chr3:113143800-113146200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:113143800-113146200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
38	chr3:113143800-113147000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
39	chr3:113143800-113147400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:113143800-113147800	Strong transcription	Ovary	ovary
41	chr3:113144000-113145800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr3:113144000-113145800	Strong transcription	Thymus	Thymus
43	chr3:113144000-113146000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:113144000-113146200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:113144000-113146200	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:113144000-113146400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:113144000-113147000	Strong transcription	Adipose Nuclei	Adipose
48	chr3:113144000-113147400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:113144200-113145800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:113144200-113146000	ZNF genes & repeats	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links