Variant report

Variant	rs4561750
Chromosome Location	chr22:31575576-31575577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31568437..31571254-chr22:31573762..31575697,3	MCF-7	breast:
2	chr22:31573119..31575986-chr22:31580233..31581989,2	MCF-7	breast:
3	chr22:31574262..31577015-chr22:31586788..31588411,2	MCF-7	breast:
4	chr22:31572111..31576977-chr22:31606424..31611296,5	MCF-7	breast:
5	chr22:31573934..31576714-chr22:31601600..31604978,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254835	Chromatin interaction
ENSG00000182541	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1005624	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1034587	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10428007	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11089491	0.81[ASN][1000 genomes]
rs12106582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12627805	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12627941	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12628752	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17220369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2027982	0.91[JPT][hapmap]
rs2072193	0.81[JPT][hapmap]
rs2073858	0.81[ASN][1000 genomes]
rs2074735	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2239905	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]
rs2239906	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2267169	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2267171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2283878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2283880	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2413041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28709894	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34184692	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3761431	0.86[CHB][hapmap]
rs3788428	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4645077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820040	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820949	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4820965	0.85[EUR][1000 genomes]
rs55737363	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55900008	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5749226	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749231	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs5749232	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5749244	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749254	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs5753487	0.91[ASN][1000 genomes]
rs5753488	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753501	0.86[ASN][1000 genomes]
rs5753518	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs5753528	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753550	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5753551	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753559	0.86[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs5753560	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753577	0.81[AMR][1000 genomes]
rs5997893	0.93[LWK][hapmap];1.00[YRI][hapmap]
rs5997898	0.91[JPT][hapmap]
rs5997940	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs61006749	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62236175	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62237396	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62237398	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62237399	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62237400	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62237404	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62237436	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68136222	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72617294	0.81[ASN][1000 genomes]
rs73158522	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs737809	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];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8135417	0.93[LWK][hapmap];1.00[YRI][hapmap]
rs886074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609263	0.87[JPT][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4561750	UTS2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31557200-31591200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr22:31557400-31579800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr22:31557400-31595200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr22:31557400-31597800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr22:31557600-31578600	Weak transcription	K562	blood
6	chr22:31557600-31591800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr22:31557800-31587000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr22:31557800-31588400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr22:31558000-31578000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr22:31558600-31583000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr22:31558600-31591400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr22:31558800-31591200	Weak transcription	Fetal Brain Male	brain
13	chr22:31558800-31606000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr22:31562000-31575600	Weak transcription	Fetal Kidney	kidney
15	chr22:31562400-31583200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr22:31562600-31578400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr22:31563000-31577400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr22:31564600-31582600	Weak transcription	Fetal Thymus	thymus
19	chr22:31566200-31583000	Weak transcription	Brain Angular Gyrus	brain
20	chr22:31566400-31575600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr22:31566400-31583000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr22:31569600-31583200	Weak transcription	Brain Anterior Caudate	brain
23	chr22:31569800-31575600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr22:31569800-31583000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr22:31569800-31591600	Weak transcription	Small Intestine	intestine
26	chr22:31570000-31606400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr22:31570200-31583000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr22:31570400-31583000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr22:31570400-31586800	Strong transcription	Fetal Stomach	stomach
30	chr22:31570400-31597800	Weak transcription	HUVEC	blood vessel
31	chr22:31571600-31576000	Enhancers	HMEC	breast
32	chr22:31571800-31582800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr22:31572200-31575600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr22:31572200-31575800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr22:31572200-31575800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr22:31572200-31576000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr22:31572200-31576000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr22:31572200-31576000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr22:31572200-31600000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr22:31572400-31576000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr22:31572600-31576000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr22:31572800-31575600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr22:31572800-31575800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr22:31572800-31575800	Enhancers	NHLF	lung
45	chr22:31572800-31576000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr22:31572800-31576000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr22:31572800-31576000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr22:31572800-31576000	Genic enhancers	Liver	Liver
49	chr22:31572800-31576000	Genic enhancers	HSMM	muscle
50	chr22:31572800-31576400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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