Variant report

Variant	rs17117873
Chromosome Location	chr1:59050994-59050995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59047843..59052771-chr1:59082760..59087529,8	MCF-7	breast:
2	chr1:59049156..59051350-chr1:59080976..59082563,2	MCF-7	breast:
3	chr1:59048457..59052619-chr1:59081708..59087602,8	MCF-7	breast:
4	chr1:59049910..59054215-chr1:59054903..59060265,8	MCF-7	breast:
5	chr1:59049755..59053628-chr1:59060314..59062387,4	MCF-7	breast:
6	chr1:59049811..59051312-chr1:59248040..59250365,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10458559	1.00[JPT][hapmap]
rs10489815	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap]
rs10789064	1.00[JPT][hapmap]
rs10789066	1.00[JPT][hapmap]
rs10889098	0.93[CEU][hapmap]
rs10889099	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10889100	1.00[JPT][hapmap]
rs10889101	1.00[JPT][hapmap]
rs10889104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1109895	1.00[JPT][hapmap]
rs1109896	1.00[JPT][hapmap]
rs11207244	0.80[YRI][hapmap]
rs11207247	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11207248	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11207251	1.00[JPT][hapmap]
rs11207252	1.00[JPT][hapmap]
rs11207255	0.86[EUR][1000 genomes]
rs11207260	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11207262	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs11207264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11207265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11207266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11207267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11207268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11581594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11582299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11583248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11584788	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11589214	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11589236	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11590757	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11590785	0.83[EUR][1000 genomes]
rs12058651	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12067296	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12067565	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12068196	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12068201	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12068391	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12068457	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12068597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12069688	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12070503	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12077340	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12077766	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12080357	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs12087583	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12092564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12097882	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12118488	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs12125391	1.00[JPT][hapmap]
rs12139475	0.93[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap]
rs12144759	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap]
rs12406405	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12568356	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17117742	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17117877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17372425	1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17461345	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2087799	1.00[JPT][hapmap]
rs3087585	0.85[GIH][hapmap];1.00[JPT][hapmap]
rs34023272	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34135541	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3893156	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3893157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41313363	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56049576	0.86[EUR][1000 genomes]
rs59607787	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59924197	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs602579	1.00[JPT][hapmap]
rs60726128	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6587820	1.00[JPT][hapmap]
rs6587821	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6663327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6664314	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6666138	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6666304	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6679808	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs6690139	1.00[ASW][hapmap];1.00[CEU][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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6704300	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67238056	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67264345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67443104	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67538366	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67673245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67805407	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68192782	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7355165	1.00[JPT][hapmap]
rs7515056	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs7536867	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7547070	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs905567	1.00[JPT][hapmap]

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	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17117873	OMA1	cis	parietal	SCAN
rs17117873	CYP2J2	cis	parietal	SCAN
rs17117873	TACSTD2	cis	multi-tissue	Pritchard
rs17117873	DAB1	cis	parietal	SCAN
rs17117873	TACSTD2	cis	Whole Blood	GTEx
rs17117873	OMA1	cis	cerebellum	SCAN
rs17117873	C8orf34	trans	cerebellum	SCAN
rs17117873	DAB1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59049000-59051000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:59049000-59051000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:59049000-59051200	Enhancers	Lung	lung
4	chr1:59049000-59051200	Enhancers	Stomach Mucosa	stomach
5	chr1:59049000-59051600	Enhancers	Primary hematopoietic stem cells	blood
6	chr1:59049000-59051600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:59049000-59052000	Enhancers	HSMMtube	muscle
8	chr1:59049000-59052200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:59049000-59052400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:59049000-59052400	Enhancers	Fetal Lung	lung
11	chr1:59049000-59052800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:59049000-59052800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:59049200-59051200	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr1:59049200-59051200	Enhancers	Rectal Smooth Muscle	rectum
15	chr1:59049200-59051400	Enhancers	K562	blood
16	chr1:59049200-59051600	Enhancers	Adipose Nuclei	Adipose
17	chr1:59049200-59052400	Enhancers	Aorta	Aorta
18	chr1:59049200-59052400	Enhancers	NHDF-Ad	bronchial
19	chr1:59049200-59052800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:59049200-59052800	Enhancers	Esophagus	oesophagus
21	chr1:59049400-59051000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:59049400-59051400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr1:59049400-59057800	Weak transcription	Gastric	stomach
24	chr1:59049600-59051200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr1:59049600-59051200	Enhancers	Colon Smooth Muscle	Colon
26	chr1:59049800-59051000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:59049800-59051200	Enhancers	Stomach Smooth Muscle	stomach
28	chr1:59049800-59051600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:59049800-59052800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:59049800-59052800	Enhancers	Ovary	ovary
31	chr1:59050000-59051800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:59050200-59051600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:59050200-59052400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:59050200-59052800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:59050200-59052800	Enhancers	HMEC	breast
36	chr1:59050200-59052800	Enhancers	HSMM	muscle
37	chr1:59050200-59053000	Enhancers	HUVEC	blood vessel
38	chr1:59050400-59051200	Enhancers	Pancreas	Pancrea
39	chr1:59050400-59051400	Enhancers	GM12878-XiMat	blood
40	chr1:59050400-59052000	Enhancers	Hela-S3	cervix
41	chr1:59050400-59052400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:59050400-59052400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:59050400-59052600	Enhancers	NH-A	brain
44	chr1:59050400-59052600	Enhancers	NHLF	lung
45	chr1:59050400-59052800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:59050600-59051800	Enhancers	A549	lung
47	chr1:59050600-59052800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:59050600-59053000	Enhancers	Osteobl	bone
49	chr1:59050600-59057400	Weak transcription	Right Atrium	heart
50	chr1:59050800-59051000	Flanking Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links