Variant report

Variant	rs4302596
Chromosome Location	chr5:43577384-43577385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43569229..43570816-chr5:43575910..43577569,2	K562	blood:
2	chr5:43555603..43557203-chr5:43575638..43578155,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NNT-5	chr5:43571510-43577741	NONHSAT101320

Variant related genes	Relation type
ENSG00000172239	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10039298	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10068155	1.00[AMR][1000 genomes]
rs10805677	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10941641	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11741521	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12514093	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4404685	1.00[AMR][1000 genomes]
rs4510596	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4513705	1.00[AMR][1000 genomes]
rs4549534	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4597976	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4640799	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4866748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4866749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4866750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6451713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6451714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6863997	1.00[AMR][1000 genomes]
rs6872851	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6874647	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6876588	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6896358	1.00[AMR][1000 genomes]
rs6897657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7717328	1.00[AMR][1000 genomes]
rs7719588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7721790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7722475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7732089	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7737410	1.00[AMR][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	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3471239	chr5:43541792-43587904	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	esv3471240	chr5:43541792-43587904	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43557800-43584600	Weak transcription	Psoas Muscle	Psoas
2	chr5:43560200-43584400	Weak transcription	K562	blood
3	chr5:43564600-43580200	Weak transcription	Fetal Kidney	kidney
4	chr5:43565400-43579000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:43565400-43601800	Weak transcription	Fetal Thymus	thymus
6	chr5:43565600-43581800	Weak transcription	Dnd41	blood
7	chr5:43566200-43590400	Weak transcription	Thymus	Thymus
8	chr5:43566400-43580200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:43566800-43586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:43567400-43602000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:43568000-43601800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr5:43568000-43602400	Weak transcription	Pancreas	Pancrea
13	chr5:43568400-43581800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:43568600-43601800	Weak transcription	Fetal Brain Female	brain
15	chr5:43569000-43601400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:43569200-43591800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr5:43570000-43582000	Weak transcription	Liver	Liver
18	chr5:43570200-43581600	Weak transcription	Left Ventricle	heart
19	chr5:43570200-43601800	Weak transcription	Right Ventricle	heart
20	chr5:43572000-43579600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr5:43572000-43591800	Weak transcription	Aorta	Aorta
22	chr5:43572000-43602400	Weak transcription	Ovary	ovary
23	chr5:43572400-43582600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:43572600-43583400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr5:43572800-43577400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:43572800-43582000	Weak transcription	Colon Smooth Muscle	Colon
27	chr5:43572800-43584400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:43573000-43582200	Weak transcription	HSMMtube	muscle
29	chr5:43573000-43582400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:43573000-43582600	Weak transcription	Adipose Nuclei	Adipose
31	chr5:43573000-43601800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:43573000-43601800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr5:43573400-43581600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr5:43573600-43583200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:43573800-43579000	Weak transcription	Fetal Intestine Large	intestine
36	chr5:43573800-43584600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:43574000-43579200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr5:43574000-43580600	Weak transcription	Lung	lung
39	chr5:43574000-43581800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:43574000-43583800	Weak transcription	Brain Angular Gyrus	brain
41	chr5:43574000-43601800	Weak transcription	Brain Anterior Caudate	brain
42	chr5:43574200-43582000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:43574400-43579000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr5:43574400-43582600	Weak transcription	Fetal Lung	lung
45	chr5:43574400-43600800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr5:43574600-43577400	Weak transcription	Fetal Heart	heart
47	chr5:43574800-43577600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr5:43575000-43584800	Weak transcription	Brain Hippocampus Middle	brain
49	chr5:43575000-43589200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:43575000-43592400	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links