Variant report

Variant	rs13158
Chromosome Location	chr22:31602187-31602188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31602004..31608593-chr22:31739507..31744494,7	MCF-7	breast:
2	chr22:31602053..31603755-chr22:31608562..31611221,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100105	Chromatin interaction
ENSG00000213888	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1034588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1034589	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs13056485	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1858821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2040533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2073857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2078803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2079431	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2106294	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2228619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2232170	0.85[CEU][hapmap]
rs2232176	0.85[CEU][hapmap]
rs2283879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2283881	0.81[ASN][1000 genomes]
rs2413033	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2413034	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2413035	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2413045	1.00[MKK][hapmap]
rs2899164	0.95[CEU][hapmap]
rs4141404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs4299418	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4603880	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs4820042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4820043	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs4820951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4820955	1.00[CEU][hapmap]
rs4820963	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs5749224	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs5749229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753500	0.88[ASN][1000 genomes]
rs5753507	0.82[ASN][1000 genomes]
rs5753521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs5753543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5753601	0.95[CEU][hapmap]
rs5997893	0.90[MEX][hapmap]
rs5997902	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5997912	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs714909	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs715510	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs737684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs737887	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs737888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8135347	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8135417	0.90[MEX][hapmap]
rs9606830	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9609264	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv979669	chr22:31600580-31602620	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13158	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs13158	SFI1	cis	cerebellum	SCAN
rs13158	RHBDD3	cis	cerebellum	SCAN
rs13158	MN1	cis	parietal	SCAN
rs13158	PISD	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31558800-31606000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr22:31570000-31606400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr22:31575800-31602600	Weak transcription	Stomach Mucosa	stomach
4	chr22:31575800-31607600	Weak transcription	Hela-S3	cervix
5	chr22:31576000-31607800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr22:31576000-31607800	Weak transcription	A549	lung
7	chr22:31579200-31607400	Weak transcription	K562	blood
8	chr22:31580800-31607600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr22:31581400-31607800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr22:31582400-31602400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr22:31582800-31603600	Strong transcription	Liver	Liver
12	chr22:31584000-31608200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:31586000-31603800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr22:31587000-31602200	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr22:31588200-31606600	Strong transcription	Fetal Stomach	stomach
16	chr22:31588400-31603400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr22:31588600-31606400	Strong transcription	Fetal Intestine Small	intestine
18	chr22:31589000-31607200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr22:31589200-31602200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr22:31589400-31603600	Strong transcription	Adipose Nuclei	Adipose
21	chr22:31589400-31605800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr22:31590600-31603200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr22:31592000-31607800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr22:31592800-31606000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr22:31593000-31607400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr22:31593200-31607600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr22:31594800-31602400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr22:31595000-31602200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr22:31595000-31602400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr22:31595000-31605200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr22:31595000-31605800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr22:31595200-31602200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr22:31595200-31602200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr22:31595200-31603400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr22:31595200-31603800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr22:31595200-31604400	Strong transcription	Fetal Intestine Large	intestine
37	chr22:31595400-31603000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr22:31595800-31606000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr22:31596200-31602400	Weak transcription	Psoas Muscle	Psoas
40	chr22:31596600-31606400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr22:31596600-31607600	Weak transcription	Fetal Kidney	kidney
42	chr22:31596800-31602200	Strong transcription	Fetal Thymus	thymus
43	chr22:31597000-31602200	Strong transcription	Fetal Brain Female	brain
44	chr22:31597000-31603600	Strong transcription	Brain Cingulate Gyrus	brain
45	chr22:31597400-31602800	Strong transcription	HSMMtube	muscle
46	chr22:31598400-31602600	Weak transcription	Fetal Lung	lung
47	chr22:31598400-31606600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr22:31598400-31606800	Weak transcription	GM12878-XiMat	blood
49	chr22:31598400-31607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr22:31598400-31607600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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