Variant report

Variant	rs4482600
Chromosome Location	chr22:30579886-30579887
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30578652..30582637-chr22:30590732..30593754,4	K562	blood:
2	chr22:30578196..30581092-chr22:30585737..30587811,3	MCF-7	breast:
3	chr22:30578823..30581368-chr22:30643689..30645542,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11552852	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13055101	0.82[EUR][1000 genomes]
rs16988149	0.94[YRI][hapmap]
rs16988244	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988291	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988303	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988304	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988333	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17648208	0.91[EUR][1000 genomes]
rs1807726	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2412980	1.00[CEU][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2412981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41278853	0.89[EUR][1000 genomes]
rs41281623	0.86[EUR][1000 genomes]
rs41281633	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4482601	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs45629133	0.82[EUR][1000 genomes]
rs4823078	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56392746	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56406718	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5753038	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5753039	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5753042	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5753043	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5763855	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763870	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763873	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763878	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58162368	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997597	0.85[MEX][hapmap];0.83[TSI][hapmap]
rs6006383	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60759987	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6518681	1.00[EUR][1000 genomes]
rs6519802	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[EUR][1000 genomes]
rs6519805	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs713916	0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7285585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7286205	1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7290175	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs737901	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883354	0.80[EUR][1000 genomes]
rs73883355	0.80[EUR][1000 genomes]
rs73883359	0.84[EUR][1000 genomes]
rs73883360	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883363	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883367	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883370	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883374	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883375	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883377	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883378	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8141471	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8142666	0.81[YRI][hapmap]
rs962322	0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv588884	chr22:30494371-30590026	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv527188	chr22:30529741-30581722	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv524628	chr22:30575163-30581722	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4482600	MTMR3	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30574400-30583600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr22:30575000-30583600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr22:30575200-30580000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr22:30575400-30584400	Enhancers	Primary hematopoietic stem cells	blood
5	chr22:30575400-30584800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr22:30575600-30583400	Weak transcription	Primary T cells from cord blood	blood
7	chr22:30575600-30584600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr22:30576200-30588000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr22:30577200-30580200	Enhancers	HepG2	liver
10	chr22:30577600-30580200	Enhancers	Fetal Lung	lung
11	chr22:30577600-30589600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr22:30577600-30591400	Enhancers	A549	lung
13	chr22:30578000-30585600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr22:30578200-30584800	Weak transcription	Spleen	Spleen
15	chr22:30578400-30580800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr22:30578400-30581000	Enhancers	Dnd41	blood
17	chr22:30578400-30581400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr22:30578600-30580600	Weak transcription	Stomach Mucosa	stomach
19	chr22:30578600-30581000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr22:30578600-30581000	Weak transcription	Small Intestine	intestine
21	chr22:30578600-30581200	Weak transcription	Fetal Stomach	stomach
22	chr22:30578800-30580000	Weak transcription	Fetal Intestine Small	intestine
23	chr22:30578800-30581000	Weak transcription	Pancreas	Pancrea
24	chr22:30579000-30580200	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr22:30579000-30585400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr22:30579200-30580000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr22:30579200-30580000	Enhancers	Fetal Thymus	thymus
28	chr22:30579200-30580000	Enhancers	K562	blood
29	chr22:30579200-30580400	Enhancers	Osteobl	bone
30	chr22:30579200-30581200	Enhancers	HSMMtube	muscle
31	chr22:30579200-30585400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr22:30579400-30580000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr22:30579400-30580200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr22:30579400-30580200	Enhancers	HMEC	breast
35	chr22:30579400-30581200	Enhancers	HSMM	muscle
36	chr22:30579400-30581600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr22:30579600-30580400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr22:30579600-30580600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr22:30579600-30580600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr22:30579600-30582000	Weak transcription	Fetal Intestine Large	intestine
41	chr22:30579600-30584800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr22:30579600-30591400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr22:30579800-30580000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr22:30579800-30580000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr22:30579800-30580000	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr22:30579800-30580000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr22:30579800-30580000	Enhancers	NHLF	lung
48	chr22:30579800-30580200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr22:30579800-30580200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr22:30579800-30580200	Enhancers	Primary monocytes fromperipheralblood	blood

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