Variant report

Variant	rs2013254
Chromosome Location	chr22:31690803-31690804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31685822..31687584-chr22:31689344..31691234,2	K562	blood:
2	chr22:31689960..31693778-chr22:31698735..31700616,3	MCF-7	breast:
3	chr22:31683915..31694680-chr22:31733392..31744713,34	MCF-7	breast:
4	chr22:31689966..31691795-chr22:31696089..31697952,2	K562	blood:
5	chr22:31684664..31691252-chr22:31735490..31744100,29	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213888	Chromatin interaction
ENSG00000100100	Chromatin interaction
ENSG00000100105	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11703927	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12166373	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12167361	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056815	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13057841	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs131200	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131202	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131209	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131213	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131219	0.89[EUR][1000 genomes]
rs140074	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs140077	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2009132	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2413048	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28523714	0.84[EUR][1000 genomes]
rs28715	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28813120	0.93[EUR][1000 genomes]
rs34873968	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4820045	0.86[EUR][1000 genomes]
rs4820961	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820969	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753558	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753576	0.89[EUR][1000 genomes]
rs5997900	0.82[EUR][1000 genomes]
rs5997909	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997919	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997929	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997932	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997938	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997960	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997971	0.80[EUR][1000 genomes]
rs713947	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7285171	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7287402	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7288643	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7288735	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7289189	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7289337	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs739427	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8141987	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8143002	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9606835	0.86[EUR][1000 genomes]
rs9619187	0.98[EUR][1000 genomes]
rs9621216	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9621221	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9621227	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	23 gene(s)	inside rSNPs	diseases
3	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2013254	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs2013254	SFI1	cis	Thyroid	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31688400-31693400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr22:31688600-31691200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr22:31688600-31691400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr22:31688600-31691800	Weak transcription	Left Ventricle	heart
5	chr22:31688800-31691400	Weak transcription	A549	lung
6	chr22:31688800-31691400	Weak transcription	HMEC	breast
7	chr22:31688800-31691600	Weak transcription	Psoas Muscle	Psoas
8	chr22:31688800-31692000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr22:31688800-31692000	Weak transcription	Colonic Mucosa	Colon
10	chr22:31688800-31692400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:31688800-31692400	Weak transcription	Fetal Lung	lung
12	chr22:31688800-31693000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr22:31689000-31691400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr22:31689000-31691400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr22:31689000-31691600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr22:31689000-31691600	Enhancers	GM12878-XiMat	blood
17	chr22:31689000-31691800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr22:31689000-31696400	Weak transcription	HepG2	liver
19	chr22:31689200-31691400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:31689200-31691400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr22:31689200-31691400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr22:31689200-31691400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr22:31689200-31691400	Weak transcription	Brain Angular Gyrus	brain
24	chr22:31689200-31691400	Weak transcription	Brain Substantia Nigra	brain
25	chr22:31689200-31691600	Weak transcription	Brain Anterior Caudate	brain
26	chr22:31689200-31692600	Enhancers	Primary B cells from cord blood	blood
27	chr22:31689200-31693000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr22:31689200-31696400	Weak transcription	Liver	Liver
29	chr22:31689200-31696400	Weak transcription	Right Atrium	heart
30	chr22:31689400-31691400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr22:31689400-31691600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr22:31689400-31709000	Weak transcription	Placenta	Placenta
33	chr22:31689600-31691400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr22:31689600-31691400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr22:31689600-31692000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr22:31689800-31691200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr22:31689800-31691200	Weak transcription	NHEK	skin
38	chr22:31689800-31691400	Weak transcription	Adipose Nuclei	Adipose
39	chr22:31689800-31691400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr22:31689800-31691400	Weak transcription	HSMM	muscle
41	chr22:31689800-31691400	Weak transcription	NHDF-Ad	bronchial
42	chr22:31689800-31691600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr22:31689800-31691600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr22:31689800-31691600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr22:31689800-31691600	Weak transcription	HSMMtube	muscle
46	chr22:31689800-31691600	Weak transcription	Osteobl	bone
47	chr22:31689800-31695600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr22:31690000-31691200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr22:31690000-31691200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr22:31690000-31691200	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links