Variant report

Variant	rs2131999
Chromosome Location	chr5:43468352-43468353
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43120092..43122781-chr5:43467312..43469229,2	MCF-7	breast:
2	chr5:43467216..43470030-chr5:43556661..43559291,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172239	Chromatin interaction
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10036954	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10038608	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10045400	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10045455	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10061165	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10074682	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10447144	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10473311	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12659369	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13185343	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1389868	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1389869	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1428640	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2013173	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2132000	0.84[EUR][1000 genomes]
rs2172763	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34007811	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35710460	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35881272	0.81[EUR][1000 genomes]
rs36013953	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3776423	0.85[EUR][1000 genomes]
rs3806870	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4073848	0.82[EUR][1000 genomes]
rs4073850	0.82[EUR][1000 genomes]
rs4242099	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4308491	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4331909	0.81[EUR][1000 genomes]
rs4415083	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4541663	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4576155	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4866746	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57547662	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57597020	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6451692	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6451693	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6451695	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6451696	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6451698	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6451703	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6451704	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6451706	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67466542	0.85[EUR][1000 genomes]
rs6858942	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6861704	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6862102	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6865217	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6870018	0.82[EUR][1000 genomes]
rs6870783	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883661	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73100614	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs750582	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs750584	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7707976	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7708369	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7708443	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7724571	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7731091	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7735243	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9292883	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9686159	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9885467	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2131999	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43433800-43483400	Weak transcription	Gastric	stomach
2	chr5:43444000-43482600	Weak transcription	HMEC	breast
3	chr5:43444200-43472600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:43444800-43482600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:43448200-43471800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:43453800-43482600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:43454000-43482400	Weak transcription	Osteobl	bone
8	chr5:43454800-43482800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:43460400-43472600	Weak transcription	Fetal Kidney	kidney
10	chr5:43460600-43471600	Weak transcription	NHDF-Ad	bronchial
11	chr5:43460600-43472000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:43461000-43470000	Weak transcription	HSMMtube	muscle
13	chr5:43461000-43482400	Weak transcription	NHLF	lung
14	chr5:43461200-43482800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:43461200-43483400	Weak transcription	Pancreas	Pancrea
16	chr5:43461600-43469800	Weak transcription	HSMM	muscle
17	chr5:43462200-43474000	Weak transcription	Lung	lung
18	chr5:43462200-43482600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:43462200-43482600	Weak transcription	Fetal Stomach	stomach
20	chr5:43462200-43482800	Weak transcription	Right Ventricle	heart
21	chr5:43462400-43483000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:43462400-43483400	Weak transcription	Spleen	Spleen
23	chr5:43464200-43480000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:43465000-43470200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:43465600-43481200	Weak transcription	HepG2	liver
26	chr5:43466200-43468600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:43466200-43472800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:43466400-43468600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:43466600-43468400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:43467000-43482000	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr5:43467000-43482800	Weak transcription	Primary T cells from cord blood	blood
32	chr5:43467200-43482800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:43467400-43471600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:43467600-43468600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:43467600-43468800	Strong transcription	Left Ventricle	heart
36	chr5:43467600-43468800	ZNF genes & repeats	Ovary	ovary
37	chr5:43467600-43471600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr5:43467600-43482400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:43467800-43479800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr5:43467800-43482400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr5:43468000-43468800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:43468000-43469600	Weak transcription	A549	lung
43	chr5:43468000-43471200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:43468000-43475800	Weak transcription	Hela-S3	cervix
45	chr5:43468000-43476000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:43468000-43476000	Weak transcription	NHEK	skin
47	chr5:43468000-43480200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr5:43468000-43480200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:43468000-43482400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr5:43468000-43482600	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links