Variant report

Variant	rs17372425
Chromosome Location	chr1:59058089-59058090
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:59041326..59044486-chr1:59056548..59059729,7	MCF-7	breast:
2	chr1:59049910..59054215-chr1:59054903..59060265,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184292	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10458559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10489815	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs10789064	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10789066	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10889100	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10889101	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10889104	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1109895	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1109896	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207247	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207248	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207250	1.00[CHB][hapmap]
rs11207251	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207252	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207260	0.81[EUR][1000 genomes]
rs11207262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11207264	0.82[AMR][1000 genomes]
rs11207265	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11207266	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11207267	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11207268	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11581594	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11582299	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11583248	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11584788	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11589214	0.81[EUR][1000 genomes]
rs11589236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11590757	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs12030713	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs12058651	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12067296	0.81[EUR][1000 genomes]
rs12067565	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs12068196	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12068201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12068391	0.81[EUR][1000 genomes]
rs12068457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12068597	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12069688	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12070503	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12077340	0.81[EUR][1000 genomes]
rs12077766	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12080357	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12092564	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12097882	0.81[EUR][1000 genomes]
rs12118488	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12125391	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12139475	1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs12144759	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12568356	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17117742	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17117873	1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17117877	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17461345	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1775002	0.86[CHB][hapmap]
rs2087799	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3087585	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs34023272	0.81[EUR][1000 genomes]
rs34135541	0.81[EUR][1000 genomes]
rs3893156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3893157	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41313363	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59607787	0.81[EUR][1000 genomes]
rs602579	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs620342	1.00[CHB][hapmap]
rs6587820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6587821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6663327	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6664314	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6666138	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs6666304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6679808	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6690139	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6704300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67238056	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67264345	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67443104	0.81[EUR][1000 genomes]
rs67538366	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67673245	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67805407	0.81[EUR][1000 genomes]
rs68192782	0.81[EUR][1000 genomes]
rs7355165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7515056	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7536867	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7547070	0.81[EUR][1000 genomes]
rs905567	1.00[CHB][hapmap];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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17372425	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs17372425	TACSTD2	cis	multi-tissue	Pritchard
rs17372425	TACSTD2	cis	Whole Blood	GTEx
rs17372425	DAB1	cis	cerebellum	SCAN
rs17372425	DAB1	cis	parietal	SCAN
rs17372425	OMA1	cis	cerebellum	SCAN
rs17372425	OMA1	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59051200-59063400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr1:59054400-59059400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:59055000-59060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:59055200-59058200	Weak transcription	Fetal Lung	lung
5	chr1:59056000-59059400	Enhancers	Pancreas	Pancrea
6	chr1:59056400-59058200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:59056400-59059400	Enhancers	HMEC	breast
8	chr1:59056800-59058800	Enhancers	Aorta	Aorta
9	chr1:59056800-59058800	Enhancers	Fetal Muscle Leg	muscle
10	chr1:59056800-59059400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:59057000-59058600	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:59057000-59059600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:59057200-59059200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:59057200-59059200	Enhancers	Hela-S3	cervix
15	chr1:59057200-59059400	Enhancers	NHDF-Ad	bronchial
16	chr1:59057200-59059600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:59057400-59058600	Enhancers	Right Ventricle	heart
18	chr1:59057400-59058800	Enhancers	Lung	lung
19	chr1:59057400-59058800	Enhancers	Rectal Smooth Muscle	rectum
20	chr1:59057400-59058800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr1:59057400-59059200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:59057400-59059200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:59057400-59059200	Enhancers	HSMM	muscle
24	chr1:59057400-59059400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:59057400-59059400	Enhancers	Ovary	ovary
26	chr1:59057600-59058200	Enhancers	Placenta	Placenta
27	chr1:59057600-59058800	Enhancers	Fetal Kidney	kidney
28	chr1:59057600-59058800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:59057600-59059200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:59057600-59059200	Enhancers	Osteobl	bone
31	chr1:59057800-59058200	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr1:59057800-59058400	Enhancers	Gastric	stomach
33	chr1:59057800-59058400	Flanking Active TSS	HSMMtube	muscle
34	chr1:59057800-59058600	Weak transcription	A549	lung
35	chr1:59057800-59058800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:59057800-59058800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:59057800-59058800	Enhancers	Colon Smooth Muscle	Colon
38	chr1:59057800-59058800	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:59057800-59058800	Enhancers	Left Ventricle	heart
40	chr1:59057800-59058800	Enhancers	Psoas Muscle	Psoas
41	chr1:59057800-59058800	Enhancers	Spleen	Spleen
42	chr1:59057800-59059000	Enhancers	NH-A	brain
43	chr1:59057800-59059600	Enhancers	NHLF	lung
44	chr1:59058000-59058400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr1:59058000-59058600	Enhancers	Fetal Stomach	stomach
46	chr1:59058000-59058800	Enhancers	Right Atrium	heart
47	chr1:59058000-59058800	Enhancers	Stomach Mucosa	stomach
48	chr1:59058000-59058800	Flanking Active TSS	HUVEC	blood vessel
49	chr1:59058000-59058800	Flanking Active TSS	NHEK	skin
50	chr1:59058000-59059000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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