Variant report

Variant	rs12167333
Chromosome Location	chr22:30575812-30575813
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	chr22:30574627..30577107-chr22:30609828..30612772,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10048885	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11090598	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12168499	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12171061	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12171250	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12171263	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17648725	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1807509	0.82[AMR][1000 genomes]
rs193473	0.84[EUR][1000 genomes]
rs193481	0.86[EUR][1000 genomes]
rs1978083	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017677	0.80[EUR][1000 genomes]
rs2051764	0.80[EUR][1000 genomes]
rs2412963	0.95[CEU][hapmap]
rs28257	0.84[EUR][1000 genomes]
rs36594	0.81[AMR][1000 genomes]
rs36596	0.81[AMR][1000 genomes]
rs36598	0.81[AMR][1000 genomes]
rs36600	0.81[AMR][1000 genomes]
rs36601	0.81[AMR][1000 genomes]
rs36605	0.81[AMR][1000 genomes]
rs36607	0.81[AMR][1000 genomes]
rs3788423	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs39712	0.81[AMR][1000 genomes]
rs41162	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs41164	0.95[CEU][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap]
rs41172	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs41174	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs41175	0.85[EUR][1000 genomes]
rs41177	0.80[CEU][hapmap]
rs41179	0.84[EUR][1000 genomes]
rs4239932	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4239933	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4337577	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4823070	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5752988	0.81[AMR][1000 genomes]
rs5752993	0.82[AMR][1000 genomes]
rs5763634	0.81[AMR][1000 genomes]
rs5763644	0.81[AMR][1000 genomes]
rs5763674	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5763675	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5763680	0.80[EUR][1000 genomes]
rs5763689	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62226440	0.81[EUR][1000 genomes]
rs718772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs737904	0.81[AMR][1000 genomes]
rs737909	0.95[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs737912	0.95[CEU][hapmap]
rs7510705	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8135823	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8138286	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8141404	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs8141765	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9614162	0.85[MKK][hapmap];0.82[YRI][hapmap]
rs9620943	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9620953	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625919	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625921	0.80[CEU][hapmap]
rs9625926	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625931	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625933	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9625935	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][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
rs12167333	MTMR3	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30572000-30577400	Weak transcription	Fetal Intestine Small	intestine
2	chr22:30572200-30576200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr22:30572800-30578000	Weak transcription	Spleen	Spleen
4	chr22:30572800-30579000	Weak transcription	Fetal Brain Male	brain
5	chr22:30573200-30576400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr22:30573600-30576400	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr22:30573600-30579400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr22:30574400-30583600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr22:30574800-30579400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr22:30575000-30579800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr22:30575000-30583600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr22:30575200-30578400	Weak transcription	Fetal Thymus	thymus
13	chr22:30575200-30580000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr22:30575400-30576200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr22:30575400-30579000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr22:30575400-30584400	Enhancers	Primary hematopoietic stem cells	blood
17	chr22:30575400-30584800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr22:30575600-30577400	Weak transcription	Thymus	Thymus
19	chr22:30575600-30577600	Weak transcription	A549	lung
20	chr22:30575600-30579800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr22:30575600-30583400	Weak transcription	Primary T cells from cord blood	blood
22	chr22:30575600-30584600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr22:30575800-30576200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr22:30575800-30577800	Enhancers	Primary B cells from cord blood	blood
25	chr22:30575800-30578400	Weak transcription	Dnd41	blood

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