Variant report

Variant	rs2239905
Chromosome Location	chr22:31680624-31680625
allele	C/T
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	chr22:31679718..31681431-chr22:31684803..31686641,2	K562	blood:
3	chr22:31675823..31681003-chr22:31682955..31686672,6	MCF-7	breast:
4	chr22:31680141..31683839-chr22:31741911..31744786,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100105	Chromatin interaction
ENSG00000213888	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1005624	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1034587	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10428007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11089491	0.87[ASN][1000 genomes]
rs12106582	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12627805	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12627941	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12628752	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17220369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2027982	0.91[JPT][hapmap]
rs2072193	0.81[JPT][hapmap]
rs2073858	0.88[ASN][1000 genomes]
rs2074735	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2239906	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267169	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2267170	0.92[ASN][1000 genomes]
rs2267171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283878	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283880	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2413041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28514306	0.84[ASN][1000 genomes]
rs28709894	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34184692	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761431	0.86[CHB][hapmap]
rs3788428	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4561750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4645077	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4820040	0.89[EUR][1000 genomes]
rs4820949	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4820952	0.87[ASN][1000 genomes]
rs4820964	0.89[ASN][1000 genomes]
rs4820965	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55737363	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55900008	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749226	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5749231	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs5749232	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749237	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749244	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749254	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs5753488	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753499	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753518	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs5753528	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5753531	0.91[ASN][1000 genomes]
rs5753550	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753551	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753559	0.86[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs5753560	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753573	0.94[EUR][1000 genomes]
rs5753577	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58315696	0.85[ASN][1000 genomes]
rs5997898	0.91[JPT][hapmap]
rs5997940	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs61006749	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62236175	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62237396	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62237398	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62237399	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62237400	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62237404	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62237436	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68136222	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72617294	0.89[ASN][1000 genomes]
rs72617295	0.94[ASN][1000 genomes]
rs73158522	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs737809	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs886074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9609263	0.87[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2239905	UTS2	trans	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31654000-31685600	Strong transcription	Fetal Stomach	stomach
2	chr22:31655400-31680800	Weak transcription	K562	blood
3	chr22:31657800-31681200	Strong transcription	Adipose Nuclei	Adipose
4	chr22:31659000-31685600	Weak transcription	Psoas Muscle	Psoas
5	chr22:31666000-31682600	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr22:31666000-31684200	Strong transcription	Aorta	Aorta
7	chr22:31667000-31684600	Weak transcription	Right Atrium	heart
8	chr22:31668400-31681200	Strong transcription	NHLF	lung
9	chr22:31669000-31682200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr22:31669000-31682400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr22:31669000-31685600	Weak transcription	Fetal Brain Male	brain
12	chr22:31669000-31686000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr22:31669200-31682600	Strong transcription	Stomach Smooth Muscle	stomach
14	chr22:31670600-31681000	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr22:31671200-31684600	Weak transcription	Fetal Heart	heart
16	chr22:31671600-31681200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr22:31671800-31681000	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr22:31671800-31686200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr22:31672600-31685600	Strong transcription	Brain Germinal Matrix	brain
20	chr22:31673000-31681800	Strong transcription	Placenta	Placenta
21	chr22:31673800-31685600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr22:31674000-31681000	Strong transcription	Colonic Mucosa	Colon
23	chr22:31674000-31683800	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr22:31674200-31680800	Strong transcription	Right Ventricle	heart
25	chr22:31674200-31682600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr22:31674200-31685400	Strong transcription	Fetal Brain Female	brain
27	chr22:31674400-31686400	Weak transcription	Fetal Kidney	kidney
28	chr22:31674400-31686400	Weak transcription	NHDF-Ad	bronchial
29	chr22:31674600-31682600	Strong transcription	Rectal Smooth Muscle	rectum
30	chr22:31675400-31681400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr22:31675400-31682200	Strong transcription	Colon Smooth Muscle	Colon
32	chr22:31675400-31686400	Weak transcription	NH-A	brain
33	chr22:31675600-31680800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr22:31675600-31681000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr22:31675800-31680800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr22:31675800-31681000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr22:31675800-31681200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr22:31675800-31685000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr22:31676200-31681000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr22:31676200-31681000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr22:31676200-31682200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr22:31676400-31681000	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr22:31676400-31684600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr22:31676600-31681600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr22:31676800-31682200	Weak transcription	GM12878-XiMat	blood
46	chr22:31676800-31682200	Weak transcription	HSMMtube	muscle
47	chr22:31676800-31684800	Weak transcription	Hela-S3	cervix
48	chr22:31676800-31685000	Weak transcription	Osteobl	bone
49	chr22:31677000-31684600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr22:31677200-31680800	Weak transcription	Dnd41	blood

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