Variant report

Variant	rs4340189
Chromosome Location	chr13:40027508-40027509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs2011719	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2012553	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2148933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2182780	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2182781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4456371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4499118	0.84[AMR][1000 genomes]
rs4569130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943666	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6563706	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6563707	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7319652	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7322023	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7326279	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7330999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7337916	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs737645	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7983763	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7985325	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7996782	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7998182	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8000420	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9315688	0.84[AMR][1000 genomes]
rs943568	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548779	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9576805	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576807	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9576810	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9576811	0.84[AMR][1000 genomes]
rs9576812	0.83[AMR][1000 genomes]
rs9603543	0.80[EUR][1000 genomes]
rs9603544	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1011	chr13:40008962-40034177	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv561536	chr13:40015948-40043224	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40021800-40027800	Enhancers	Fetal Heart	heart
2	chr13:40022000-40029200	Weak transcription	Spleen	Spleen
3	chr13:40023000-40028000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr13:40023400-40035000	Weak transcription	Aorta	Aorta
5	chr13:40024000-40028000	Enhancers	Brain Hippocampus Middle	brain
6	chr13:40024600-40027600	Enhancers	Adipose Nuclei	Adipose
7	chr13:40024600-40028000	Enhancers	Colon Smooth Muscle	Colon
8	chr13:40024600-40028200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr13:40024600-40028200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr13:40025000-40027600	Enhancers	Brain Anterior Caudate	brain
11	chr13:40025000-40028000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr13:40025200-40028000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr13:40025400-40028000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr13:40025400-40028000	Enhancers	Brain Germinal Matrix	brain
15	chr13:40025400-40028200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr13:40025600-40028200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:40025600-40028200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr13:40025600-40033400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr13:40026000-40028200	Enhancers	Ovary	ovary
20	chr13:40026400-40027600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr13:40026600-40028000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:40026600-40028200	Enhancers	Left Ventricle	heart
23	chr13:40026600-40028200	Enhancers	Right Ventricle	heart
24	chr13:40026600-40029400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr13:40026600-40029600	Weak transcription	HSMM	muscle
26	chr13:40026600-40033400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr13:40026800-40027800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr13:40026800-40027800	Weak transcription	Right Atrium	heart
29	chr13:40026800-40028000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr13:40026800-40029200	Weak transcription	Lung	lung
31	chr13:40027000-40028200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr13:40027000-40028200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr13:40027000-40028200	Enhancers	Rectal Smooth Muscle	rectum
34	chr13:40027200-40028000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr13:40027200-40028000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr13:40027200-40033200	Weak transcription	HSMMtube	muscle
37	chr13:40027400-40027800	Weak transcription	Psoas Muscle	Psoas
38	chr13:40027400-40029400	Weak transcription	Brain Substantia Nigra	brain
39	chr13:40027400-40029600	Weak transcription	Fetal Lung	lung
40	chr13:40027400-40033400	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links