Variant report

Variant	rs2236589
Chromosome Location	chr1:179783922-179783923
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179783615..179784508-chr1:180137753..180138564,2	K562	blood:
2	chr1:179675234..179676215-chr1:179783594..179784662,4	MCF-7	breast:
3	chr1:179675242..179676113-chr1:179783547..179784540,8	K562	blood:
4	chr1:179783903..179786438-chr1:179821262..179823436,2	K562	blood:
5	chr1:179783164..179785606-chr1:179786239..179787962,2	K562	blood:
6	chr1:179220959..179221479-chr1:179783428..179784123,2	MCF-7	breast:
7	chr1:179776435..179778969-chr1:179781392..179784321,2	MCF-7	breast:
8	chr1:179775866..179779204-chr1:179781630..179784471,3	MCF-7	breast:
9	chr1:179782871..179785322-chr1:179845479..179847389,2	K562	blood:
10	chr1:179781708..179784126-chr1:179850566..179852565,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TOR1AIP2-2	chr1:179782871-179785662	NONHSAT008207
2	lnc-TOR1AIP2-2	chr1:179782871-179785662	NONHSAT008208

No data

Variant related genes	Relation type
ENSG00000272906	Chromatin interaction
ENSG00000169905	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000229407	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1148824	0.81[CEU][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap]
rs1148825	0.86[GIH][hapmap]
rs1281421	0.84[GIH][hapmap]
rs1281422	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2647226	0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2777913	0.81[CEU][hapmap]
rs2777914	0.81[CEU][hapmap]
rs2777920	0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2794579	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs2794586	0.82[GIH][hapmap]
rs2794589	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3845386	0.82[GIH][hapmap]
rs4320747	0.84[GIH][hapmap]
rs6425594	0.84[GIH][hapmap]
rs6658638	0.83[AMR][1000 genomes]
rs6684425	0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs904272	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][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	nsv1009961	chr1:179714247-179790110	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1011407	chr1:179733193-179799430	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv520418	chr1:179761601-179794602	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv519307	chr1:179766086-179795505	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179782800-179784200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:179783400-179784000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
3	chr1:179783400-179784000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr1:179783400-179784000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr1:179783400-179784000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr1:179783400-179784000	Enhancers	Placenta	Placenta
7	chr1:179783400-179784800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr1:179783400-179785000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:179783400-179785000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:179783600-179784000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
11	chr1:179783600-179784000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:179783600-179784000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:179783600-179784000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr1:179783600-179784000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr1:179783600-179784000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
16	chr1:179783600-179784000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:179783600-179784000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:179783600-179784000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr1:179783600-179784000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr1:179783600-179784000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:179783600-179784000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:179783600-179784000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:179783600-179784000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:179783600-179784000	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr1:179783600-179784000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:179783600-179784000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr1:179783600-179784000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr1:179783600-179784000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
29	chr1:179783600-179784000	Flanking Active TSS	Fetal Thymus	thymus
30	chr1:179783600-179784000	Flanking Active TSS	GM12878-XiMat	blood
31	chr1:179783600-179784000	Flanking Bivalent TSS/Enh	HepG2	liver
32	chr1:179783600-179784000	Flanking Active TSS	NHDF-Ad	bronchial
33	chr1:179783600-179784000	Flanking Active TSS	NHEK	skin
34	chr1:179783600-179784000	Flanking Bivalent TSS/Enh	Osteobl	bone
35	chr1:179783600-179784200	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr1:179783600-179784200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:179783600-179784200	Active TSS	Esophagus	oesophagus
38	chr1:179783600-179784200	Enhancers	Left Ventricle	heart
39	chr1:179783600-179784200	Enhancers	Psoas Muscle	Psoas
40	chr1:179783600-179784200	Active TSS	HSMM	muscle
41	chr1:179783600-179784400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr1:179783600-179784400	Active TSS	Gastric	stomach
43	chr1:179783600-179784400	Active TSS	Rectal Smooth Muscle	rectum
44	chr1:179783600-179784600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:179783600-179784600	Active TSS	A549	lung
46	chr1:179783600-179784800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
47	chr1:179783600-179784800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
48	chr1:179783600-179784800	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr1:179783600-179784800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
50	chr1:179783600-179784800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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