Variant report

Variant	rs56354026
Chromosome Location	chr3:156438321-156438322
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156436539..156440034-chr3:156533974..156536493,3	MCF-7	breast:
2	chr3:156407850..156409801-chr3:156437038..156439312,2	K562	blood:
3	chr3:156391548..156394303-chr3:156435239..156439142,4	MCF-7	breast:
4	chr3:156419995..156422332-chr3:156437118..156439741,2	K562	blood:

Variant related genes	Relation type
ENSG00000240875	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10513495	0.92[EUR][1000 genomes]
rs12636629	0.84[EUR][1000 genomes]
rs1367312	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1529581	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17373227	0.97[EUR][1000 genomes]
rs41366145	0.84[EUR][1000 genomes]
rs4364127	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55686038	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748213	0.92[ASN][1000 genomes]
rs56128116	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56152727	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56245561	0.95[EUR][1000 genomes]
rs56357051	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56836190	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56960846	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57483705	0.84[EUR][1000 genomes]
rs58263861	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58822703	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59689193	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60032002	1.00[ASN][1000 genomes]
rs60178381	0.82[ASN][1000 genomes]
rs73012038	0.82[EUR][1000 genomes]
rs73012046	0.82[EUR][1000 genomes]
rs73013957	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73019737	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019748	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019749	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs891463	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919520	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56354026	LINC00886	cis	Thyroid	GTEx
rs56354026	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs56354026	LINC00886	cis	Artery Tibial	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156395600-156438600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:156396600-156441000	Weak transcription	Lung	lung
3	chr3:156416000-156443000	Weak transcription	Aorta	Aorta
4	chr3:156422800-156438600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:156422800-156442800	Weak transcription	Psoas Muscle	Psoas
6	chr3:156423000-156443200	Weak transcription	Small Intestine	intestine
7	chr3:156423000-156445800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:156424000-156440800	Weak transcription	NHLF	lung
9	chr3:156424200-156443000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:156424200-156445800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:156424400-156438400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:156424400-156438400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:156424400-156438600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:156424400-156438600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:156424400-156438600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:156424800-156438400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:156426600-156446000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:156428200-156438400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:156428400-156439200	Weak transcription	K562	blood
20	chr3:156428600-156445200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:156428800-156438600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:156429000-156438600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:156429000-156443000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:156429200-156438400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:156429200-156439000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:156429200-156439200	Weak transcription	NHDF-Ad	bronchial
27	chr3:156433400-156440000	Weak transcription	GM12878-XiMat	blood
28	chr3:156433800-156440800	Weak transcription	Left Ventricle	heart
29	chr3:156433800-156445000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:156435200-156444800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:156436000-156438600	Weak transcription	Osteobl	bone
32	chr3:156436000-156440800	Weak transcription	NH-A	brain
33	chr3:156436200-156446200	Weak transcription	Gastric	stomach
34	chr3:156436400-156440200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:156436600-156438800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:156436600-156440200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:156436600-156445800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:156436800-156439600	Weak transcription	Hela-S3	cervix
39	chr3:156436800-156443200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:156437000-156438400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:156437000-156438400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:156437000-156438600	Weak transcription	A549	lung
43	chr3:156437000-156440400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:156437000-156440400	Weak transcription	NHEK	skin
45	chr3:156437000-156443000	Weak transcription	HUVEC	blood vessel
46	chr3:156437000-156446000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:156437200-156438800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:156437200-156438800	Weak transcription	HSMMtube	muscle
49	chr3:156437200-156440000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:156437200-156440800	Strong transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links