Variant report

Variant	rs2413046
Chromosome Location	chr22:31665909-31665910
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:31665883-31666244	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr22:31665887-31666628	H1-hESC	embryonic stem cell:	n/a	chr22:31666458-31666468
3	CEBPB	chr22:31665862-31666251	MCF-7	breast:	n/a	n/a
4	CEBPB	chr22:31665833-31666489	H1-hESC	embryonic stem cell:	n/a	n/a
5	TBP	chr22:31665889-31666190	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZNF263	chr22:31665906-31667144	HEK293-T-REx	kidney:	n/a	chr22:31666754-31666763
7	CEBPB	chr22:31665809-31666132	MCF-7	breast:	n/a	n/a
8	ATF2	chr22:31665848-31666206	H1-hESC	embryonic stem cell:	n/a	n/a
9	SP1	chr22:31665722-31666305	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr22:31665899-31666332	ECC-1	luminal epithelium:	n/a	n/a
11	CHD2	chr22:31665854-31666248	H1-hESC	embryonic stem cell:	n/a	n/a
12	SP1	chr22:31665729-31666306	H1-hESC	embryonic stem cell:	n/a	n/a
13	CEBPB	chr22:31665884-31666195	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31664794..31666350-chr22:31685084..31688102,3	MCF-7	breast:
2	chr22:31608032..31610413-chr22:31664512..31666817,2	K562	blood:

Variant related genes	Relation type
LIMK2	TF binding region
ENSG00000100100	Chromatin interaction
ENSG00000182541	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1034588	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1034589	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12152166	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13054220	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs131205	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1858821	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040533	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2078803	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2079431	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2106294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2228619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283879	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283881	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2413032	0.84[EUR][1000 genomes]
rs2413033	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2413034	0.88[EUR][1000 genomes]
rs2413035	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2413047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413049	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4141404	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4299418	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4603880	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820042	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4820043	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820951	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4820962	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820963	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749224	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs5749229	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5749243	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5753500	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5753505	0.81[EUR][1000 genomes]
rs5753507	0.86[EUR][1000 genomes]
rs5753521	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753543	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59315359	0.82[EUR][1000 genomes]
rs5997902	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5997912	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997913	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5997933	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5997939	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997949	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71324184	0.84[EUR][1000 genomes]
rs714909	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs715510	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7287267	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737684	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737887	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737888	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8135344	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8135347	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8138596	0.83[EUR][1000 genomes]
rs9606830	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9606831	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609254	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609257	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9609264	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609265	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609266	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609267	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9609268	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9621235	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2413046	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs2413046	SFI1	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31644600-31668600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr22:31645000-31668400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr22:31645000-31668600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr22:31645000-31677600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr22:31645200-31667000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr22:31650200-31666200	Strong transcription	HepG2	liver
7	chr22:31650200-31675600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr22:31650200-31679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr22:31650600-31676400	Weak transcription	Hela-S3	cervix
10	chr22:31651400-31670200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr22:31651600-31667000	Weak transcription	Fetal Heart	heart
12	chr22:31651800-31675800	Strong transcription	HMEC	breast
13	chr22:31652800-31675800	Strong transcription	NHEK	skin
14	chr22:31652800-31679400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr22:31653000-31667400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr22:31653400-31670200	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr22:31653600-31668400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr22:31653800-31667800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr22:31653800-31668600	Weak transcription	Fetal Brain Male	brain
20	chr22:31653800-31670800	Strong transcription	Primary T cells from cord blood	blood
21	chr22:31653800-31676200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr22:31654000-31668400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr22:31654000-31668400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr22:31654000-31668400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr22:31654000-31668800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr22:31654000-31669000	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr22:31654000-31676400	Strong transcription	Thymus	Thymus
28	chr22:31654000-31680400	Strong transcription	Lung	lung
29	chr22:31654000-31685600	Strong transcription	Fetal Stomach	stomach
30	chr22:31654200-31668600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr22:31654200-31677200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr22:31654200-31680200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr22:31654200-31680400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr22:31654400-31679600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr22:31655200-31668600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr22:31655400-31680800	Weak transcription	K562	blood
37	chr22:31656600-31671000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr22:31656800-31666000	Weak transcription	Fetal Kidney	kidney
39	chr22:31656800-31668600	Weak transcription	NHDF-Ad	bronchial
40	chr22:31656800-31674000	Weak transcription	Brain Angular Gyrus	brain
41	chr22:31657800-31681200	Strong transcription	Adipose Nuclei	Adipose
42	chr22:31658800-31666000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr22:31659000-31685600	Weak transcription	Psoas Muscle	Psoas
44	chr22:31659400-31678600	Strong transcription	Fetal Muscle Leg	muscle
45	chr22:31660400-31666000	Strong transcription	Fetal Intestine Small	intestine
46	chr22:31660600-31667000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr22:31660600-31670800	Strong transcription	Duodenum Mucosa	Duodenum
48	chr22:31661400-31668000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr22:31661400-31671800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr22:31661400-31677800	Weak transcription	A549	lung

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