Variant report

Variant	rs2040533
Chromosome Location	chr22:31679110-31679111
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31674730..31677277-chr22:31677970..31680795,3	K562	blood:
2	chr22:31678127..31679737-chr22:31693354..31695719,2	MCF-7	breast:
3	chr22:31675823..31681003-chr22:31682955..31686672,6	MCF-7	breast:
4	chr22:31677171..31679291-chr22:31685121..31687436,2	K562	blood:
5	chr22:31635408..31638175-chr22:31677816..31680372,2	MCF-7	breast:
6	chr22:31671853..31673887-chr22:31677470..31679780,2	MCF-7	breast:
7	chr22:31675502..31680244-chr22:31686864..31689429,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100100	Chromatin interaction
ENSG00000228839	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1034588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1034589	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12152166	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13054220	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13056485	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs131205	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1858821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2078803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2079431	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2106294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2228619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232170	0.90[CEU][hapmap]
rs2232176	0.90[CEU][hapmap]
rs2273249	0.95[CEU][hapmap]
rs2273251	0.95[CEU][hapmap]
rs2283879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283881	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2413032	0.85[EUR][1000 genomes]
rs2413033	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2413034	0.89[EUR][1000 genomes]
rs2413035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2413046	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413047	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413049	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2899164	0.95[CEU][hapmap]
rs4141404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4299418	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4603880	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4820043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4820955	1.00[CEU][hapmap]
rs4820962	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820963	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749224	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs5749229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5749243	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5753500	0.88[EUR][1000 genomes]
rs5753505	0.81[EUR][1000 genomes]
rs5753507	0.87[EUR][1000 genomes]
rs5753521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753601	0.95[CEU][hapmap]
rs5753609	0.90[CEU][hapmap]
rs5753632	0.95[CEU][hapmap]
rs5753639	0.95[CEU][hapmap]
rs59315359	0.83[EUR][1000 genomes]
rs5997902	0.90[EUR][1000 genomes]
rs5997912	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997949	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71324184	0.84[EUR][1000 genomes]
rs714909	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs715510	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7285619	0.95[CEU][hapmap]
rs7287267	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737887	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs738657	0.95[CEU][hapmap]
rs8135344	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8135347	0.89[EUR][1000 genomes]
rs8138596	0.84[EUR][1000 genomes]
rs9606830	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9606831	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9606839	0.95[CEU][hapmap]
rs9606843	0.94[CEU][hapmap]
rs9609254	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609257	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9609264	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609265	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609266	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609267	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9609268	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9621235	0.83[AMR][1000 genomes];0.89[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
rs2040533	SFI1	cis	Thyroid	GTEx
rs2040533	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31650200-31679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr22:31652800-31679400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr22:31654000-31680400	Strong transcription	Lung	lung
4	chr22:31654000-31685600	Strong transcription	Fetal Stomach	stomach
5	chr22:31654200-31680200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr22:31654200-31680400	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr22:31654400-31679600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr22:31655400-31680800	Weak transcription	K562	blood
9	chr22:31657800-31681200	Strong transcription	Adipose Nuclei	Adipose
10	chr22:31659000-31685600	Weak transcription	Psoas Muscle	Psoas
11	chr22:31665600-31679400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr22:31666000-31682600	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr22:31666000-31684200	Strong transcription	Aorta	Aorta
14	chr22:31667000-31684600	Weak transcription	Right Atrium	heart
15	chr22:31668400-31681200	Strong transcription	NHLF	lung
16	chr22:31668800-31680400	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr22:31669000-31679400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr22:31669000-31680200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr22:31669000-31680400	Strong transcription	Brain Anterior Caudate	brain
20	chr22:31669000-31682200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr22:31669000-31682400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr22:31669000-31685600	Weak transcription	Fetal Brain Male	brain
23	chr22:31669000-31686000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr22:31669200-31682600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr22:31669600-31680400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr22:31670000-31680600	Strong transcription	Primary B cells from peripheral blood	blood
27	chr22:31670600-31681000	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr22:31671200-31684600	Weak transcription	Fetal Heart	heart
29	chr22:31671400-31679200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr22:31671400-31680200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr22:31671600-31679400	Strong transcription	Fetal Intestine Large	intestine
32	chr22:31671600-31679600	Strong transcription	Fetal Intestine Small	intestine
33	chr22:31671600-31681200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr22:31671800-31681000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr22:31671800-31686200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr22:31672000-31680400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr22:31672600-31685600	Strong transcription	Brain Germinal Matrix	brain
38	chr22:31672800-31680600	Strong transcription	Primary B cells from cord blood	blood
39	chr22:31673000-31681800	Strong transcription	Placenta	Placenta
40	chr22:31673600-31679400	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr22:31673800-31679400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr22:31673800-31680200	Strong transcription	Brain Substantia Nigra	brain
43	chr22:31673800-31685600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr22:31674000-31680400	Strong transcription	Brain Hippocampus Middle	brain
45	chr22:31674000-31680600	Strong transcription	Brain Angular Gyrus	brain
46	chr22:31674000-31681000	Strong transcription	Colonic Mucosa	Colon
47	chr22:31674000-31683800	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr22:31674200-31680800	Strong transcription	Right Ventricle	heart
49	chr22:31674200-31682600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr22:31674200-31685400	Strong transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links