Variant report

Variant	rs2280969
Chromosome Location	chr2:32290147-32290148
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:32286352..32290626-chr2:32388602..32393371,12	K562	blood:
2	chr2:32286363..32290764-chr2:32387862..32393371,13	K562	blood:
3	chr2:32288902..32290872-chr2:32375784..32377323,2	MCF-7	breast:
4	chr2:32262818..32267061-chr2:32286978..32290820,6	MCF-7	breast:
5	chr2:32263531..32265848-chr2:32287148..32290470,4	K562	blood:
6	chr2:32233309..32238481-chr2:32286150..32290599,7	MCF-7	breast:
7	chr2:32235889..32238860-chr2:32287017..32290574,4	MCF-7	breast:
8	chr2:32287157..32290220-chr2:32389830..32392599,3	MCF-7	breast:
9	chr2:32262396..32266546-chr2:32286416..32291415,12	K562	blood:
10	chr2:32263267..32267327-chr2:32283931..32290396,13	MCF-7	breast:
11	chr2:32232898..32237970-chr2:32287390..32290443,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152683	Chromatin interaction
ENSG00000162959	Chromatin interaction
ENSG00000162961	Chromatin interaction
ENSG00000272716	Chromatin interaction
ENSG00000271228	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10490360	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11124274	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11124275	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11124276	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11124277	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11676938	0.91[ASN][1000 genomes]
rs11681731	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11683931	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11686061	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11691879	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12465124	0.84[ASN][1000 genomes]
rs12474443	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12611678	0.82[ASN][1000 genomes]
rs12617289	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12617290	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12618002	0.81[ASN][1000 genomes]
rs12620922	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12989936	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12992743	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13000753	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13007972	0.82[ASN][1000 genomes]
rs13008192	0.80[ASN][1000 genomes]
rs13017189	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13022197	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13024004	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13029752	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13033833	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13431540	0.82[ASN][1000 genomes]
rs17767988	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1904489	0.80[ASN][1000 genomes]
rs212739	0.80[EUR][1000 genomes]
rs216538	0.93[ASN][1000 genomes]
rs216544	0.89[ASN][1000 genomes]
rs2235134	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280967	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294179	0.82[ASN][1000 genomes]
rs2365555	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2365558	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34856365	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35650265	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36014814	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3752916	0.82[ASN][1000 genomes]
rs3769604	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769606	0.91[ASN][1000 genomes]
rs454119	0.88[ASN][1000 genomes]
rs467523	0.95[ASN][1000 genomes]
rs469305	0.81[ASN][1000 genomes]
rs4952247	0.81[EUR][1000 genomes]
rs4952249	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4952250	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56208031	0.81[ASN][1000 genomes]
rs56740303	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62142080	0.81[ASN][1000 genomes]
rs6543647	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6543649	0.81[EUR][1000 genomes]
rs660393	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67157050	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6737500	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6738349	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6747488	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6748621	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6749336	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6752375	0.91[ASN][1000 genomes]
rs6758024	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6760105	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6761417	0.81[ASN][1000 genomes]
rs678251	0.92[ASN][1000 genomes]
rs72862234	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7370704	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7559964	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7561519	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7566162	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7573543	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7575139	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7577408	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7577696	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7581032	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7581340	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7586448	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7600173	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7600885	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7601267	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7604559	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7605242	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7608127	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7608229	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9677104	0.81[ASN][1000 genomes]
rs9750659	0.82[ASN][1000 genomes]
rs9752631	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32287400-32290200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:32287400-32290200	Active TSS	Fetal Intestine Large	intestine
3	chr2:32287400-32290200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr2:32287600-32290200	Active TSS	Fetal Thymus	thymus
5	chr2:32287600-32290200	Active TSS	Right Ventricle	heart
6	chr2:32287800-32290200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr2:32287800-32290200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:32287800-32290200	Active TSS	GM12878-XiMat	blood
9	chr2:32287800-32290400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr2:32287800-32290400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:32288000-32290200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:32288000-32290200	Active TSS	Fetal Intestine Small	intestine
13	chr2:32288000-32290400	Active TSS	Rectal Smooth Muscle	rectum
14	chr2:32288000-32290400	Active TSS	HMEC	breast
15	chr2:32289400-32290400	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr2:32289400-32290400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:32289400-32290800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr2:32289400-32290800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr2:32289600-32290200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:32289600-32290200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:32289600-32290200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr2:32289600-32290200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr2:32289600-32290200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:32289600-32290200	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr2:32289600-32290200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr2:32289600-32290200	Flanking Active TSS	A549	lung
27	chr2:32289600-32290200	Flanking Active TSS	NHEK	skin
28	chr2:32289600-32290400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:32289600-32290400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr2:32289600-32290400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:32289600-32290400	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr2:32289600-32290400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr2:32289600-32291000	Flanking Active TSS	Dnd41	blood
34	chr2:32289600-32291200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:32289600-32330800	Weak transcription	Spleen	Spleen
36	chr2:32289800-32290200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:32289800-32290200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:32289800-32290200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr2:32289800-32290200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:32289800-32290200	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr2:32289800-32290200	Weak transcription	Esophagus	oesophagus
42	chr2:32289800-32290200	Weak transcription	Gastric	stomach
43	chr2:32289800-32290200	Weak transcription	Left Ventricle	heart
44	chr2:32289800-32290200	Weak transcription	Lung	lung
45	chr2:32289800-32290200	Weak transcription	Right Atrium	heart
46	chr2:32289800-32290200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:32289800-32290200	Flanking Active TSS	HepG2	liver
48	chr2:32289800-32290200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr2:32289800-32290200	Active TSS	NH-A	brain
50	chr2:32289800-32290400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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