Variant report

Variant	rs12451054
Chromosome Location	chr17:16989848-16989849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16989031..16991528-chr17:17000273..17002775,2	MCF-7	breast:
2	chr17:16944252..16948072-chr17:16988311..16992318,5	MCF-7	breast:
3	chr17:16984318..16990325-chr17:16990439..16995530,6	K562	blood:

Variant related genes	Relation type
ENSG00000133030	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1047805	0.90[AMR][1000 genomes]
rs10852843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852844	0.95[AMR][1000 genomes]
rs10852845	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10852846	0.90[AMR][1000 genomes]
rs11078364	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11078365	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11078366	0.90[ASN][1000 genomes]
rs11078370	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078371	0.95[AMR][1000 genomes]
rs11078372	0.95[AMR][1000 genomes]
rs11078373	0.90[AMR][1000 genomes]
rs11078375	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1110504	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1110505	0.90[AMR][1000 genomes]
rs11651460	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11651938	0.90[AMR][1000 genomes]
rs11651988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11652079	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11652674	0.87[EUR][1000 genomes]
rs11652678	0.90[AMR][1000 genomes]
rs11652756	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11652936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654247	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11654360	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11654562	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11658084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11658904	0.88[ASN][1000 genomes]
rs12450109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12450213	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12450238	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12450467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452303	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12452802	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12601325	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12602124	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602867	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16961288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16961412	0.88[AMR][1000 genomes]
rs1877631	0.82[ASN][1000 genomes]
rs2292526	0.86[AMR][1000 genomes]
rs3744125	0.90[AMR][1000 genomes]
rs3744127	0.90[AMR][1000 genomes]
rs3744132	0.90[AMR][1000 genomes]
rs3744133	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3744136	0.90[AMR][1000 genomes]
rs3744140	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3826305	0.88[AMR][1000 genomes]
rs4073940	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074611	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074612	0.95[AMR][1000 genomes]
rs4074819	0.90[AMR][1000 genomes]
rs4264448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4283273	0.90[AMR][1000 genomes]
rs4321246	0.86[AMR][1000 genomes]
rs4606773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4621033	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985698	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985703	0.90[AMR][1000 genomes]
rs4985712	0.85[ASN][1000 genomes]
rs4985714	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985715	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985723	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985739	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4985744	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4985747	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55751545	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56009207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57812549	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58326998	0.90[AMR][1000 genomes]
rs58472573	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58814183	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59394251	0.90[AMR][1000 genomes]
rs60128647	0.95[AMR][1000 genomes]
rs61018209	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7207187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7210339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217970	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7223583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7223686	0.90[ASN][1000 genomes]
rs7223924	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73979053	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73979054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73979055	0.96[AFR][1000 genomes]
rs73979058	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73979060	0.95[AMR][1000 genomes]
rs73979061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064991	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8066111	0.90[AMR][1000 genomes]
rs8067563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8075751	0.85[ASN][1000 genomes]
rs9910011	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059280	chr17:16975059-17017957	Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12451054	M-RIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16952600-16996400	Weak transcription	Fetal Brain Male	brain
2	chr17:16959600-16992000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr17:16973600-16997600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr17:16974000-16995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr17:16977200-16991200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr17:16977400-16992400	Strong transcription	Hela-S3	cervix
7	chr17:16978600-16991000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:16978800-16996800	Strong transcription	Dnd41	blood
9	chr17:16979200-16991400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:16979400-16990000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr17:16979400-16991200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr17:16979400-16991400	Strong transcription	Primary T cells from cord blood	blood
13	chr17:16979800-16992200	Strong transcription	Thymus	Thymus
14	chr17:16981600-16991600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr17:16981600-16995000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:16981600-16995400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr17:16981800-16990200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:16981800-16990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr17:16981800-16992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr17:16981800-16995400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr17:16982000-16990600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:16982000-16995400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr17:16982000-16995400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr17:16982000-16995600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr17:16982600-16990400	Weak transcription	Brain Germinal Matrix	brain
26	chr17:16982600-16990600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr17:16982800-16995400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:16983000-16996400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr17:16983400-16995400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr17:16985000-16990200	Weak transcription	Fetal Heart	heart
31	chr17:16985000-16990400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr17:16985000-16990800	Weak transcription	Brain Substantia Nigra	brain
33	chr17:16985000-16991800	Weak transcription	Colonic Mucosa	Colon
34	chr17:16985200-16990000	Weak transcription	Right Atrium	heart
35	chr17:16985200-16991800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:16985200-16992000	Weak transcription	Small Intestine	intestine
37	chr17:16985200-16993200	Strong transcription	Fetal Intestine Small	intestine
38	chr17:16985200-16996000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr17:16985400-16990800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr17:16985400-16991000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr17:16985400-16993800	Strong transcription	Fetal Stomach	stomach
42	chr17:16985600-16990000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr17:16985600-16996800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr17:16985800-16991600	Strong transcription	Fetal Thymus	thymus
45	chr17:16985800-16991800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:16986000-16990000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:16986000-16990000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr17:16986000-16990200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr17:16986000-16990800	Strong transcription	HSMM	muscle
50	chr17:16986000-16991200	Strong transcription	Rectal Mucosa Donor 29	rectum

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