Variant report

Variant	rs3893157
Chromosome Location	chr1:59050480-59050481
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: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10458559	0.81[ASN][1000 genomes]
rs10789064	0.81[ASN][1000 genomes]
rs10789066	0.81[ASN][1000 genomes]
rs10889099	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10889100	0.81[ASN][1000 genomes]
rs10889101	0.81[ASN][1000 genomes]
rs10889104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1109895	0.81[ASN][1000 genomes]
rs1109896	0.81[ASN][1000 genomes]
rs11207248	0.83[EUR][1000 genomes]
rs11207250	0.81[ASN][1000 genomes]
rs11207251	0.81[ASN][1000 genomes]
rs11207252	0.81[ASN][1000 genomes]
rs11207253	0.81[ASN][1000 genomes]
rs11207254	0.81[ASN][1000 genomes]
rs11207255	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207260	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207262	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584788	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11589214	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11589236	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11590757	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11590785	0.83[EUR][1000 genomes]
rs12058651	0.85[EUR][1000 genomes]
rs12067296	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067565	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068196	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068391	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068457	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069688	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077340	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12077766	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12087583	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12092564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097882	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12125391	0.81[ASN][1000 genomes]
rs12142098	0.81[ASN][1000 genomes]
rs12406405	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568356	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17117742	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17117873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17117877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17372425	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17461345	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2087799	0.81[ASN][1000 genomes]
rs232841	0.97[ASN][1000 genomes]
rs232842	0.97[ASN][1000 genomes]
rs232844	0.97[ASN][1000 genomes]
rs232847	0.97[ASN][1000 genomes]
rs232848	0.94[ASN][1000 genomes]
rs232849	0.94[ASN][1000 genomes]
rs2406784	0.81[ASN][1000 genomes]
rs34023272	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34135541	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3893156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41313363	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56049576	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs562166	0.94[ASN][1000 genomes]
rs584579	0.94[ASN][1000 genomes]
rs59607787	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59924197	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs602579	0.94[ASN][1000 genomes]
rs603031	0.94[ASN][1000 genomes]
rs60726128	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61779295	0.97[ASN][1000 genomes]
rs61779296	0.97[ASN][1000 genomes]
rs620342	0.94[ASN][1000 genomes]
rs627218	0.94[ASN][1000 genomes]
rs6663327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664314	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6666138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666304	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67238056	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67264345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67443104	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67538366	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67673245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67805407	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68192782	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7546900	0.81[ASN][1000 genomes]
rs7547070	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs905567	0.81[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3893157	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs3893157	TACSTD2	cis	Whole Blood	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59049000-59050800	Enhancers	Placenta	Placenta
2	chr1:59049000-59050800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr1:59049000-59051000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:59049000-59051000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr1:59049000-59051200	Enhancers	Lung	lung
6	chr1:59049000-59051200	Enhancers	Stomach Mucosa	stomach
7	chr1:59049000-59051600	Enhancers	Primary hematopoietic stem cells	blood
8	chr1:59049000-59051600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:59049000-59052000	Enhancers	HSMMtube	muscle
10	chr1:59049000-59052200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:59049000-59052400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:59049000-59052400	Enhancers	Fetal Lung	lung
13	chr1:59049000-59052800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:59049000-59052800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:59049200-59050600	Enhancers	Fetal Muscle Leg	muscle
16	chr1:59049200-59050600	Enhancers	HepG2	liver
17	chr1:59049200-59050800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:59049200-59051200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr1:59049200-59051200	Enhancers	Rectal Smooth Muscle	rectum
20	chr1:59049200-59051400	Enhancers	K562	blood
21	chr1:59049200-59051600	Enhancers	Adipose Nuclei	Adipose
22	chr1:59049200-59052400	Enhancers	Aorta	Aorta
23	chr1:59049200-59052400	Enhancers	NHDF-Ad	bronchial
24	chr1:59049200-59052800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:59049200-59052800	Enhancers	Esophagus	oesophagus
26	chr1:59049400-59050800	Weak transcription	Spleen	Spleen
27	chr1:59049400-59051000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:59049400-59051400	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:59049400-59057800	Weak transcription	Gastric	stomach
30	chr1:59049600-59051200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr1:59049600-59051200	Enhancers	Colon Smooth Muscle	Colon
32	chr1:59049800-59050600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:59049800-59050600	Enhancers	Right Atrium	heart
34	chr1:59049800-59051000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr1:59049800-59051200	Enhancers	Stomach Smooth Muscle	stomach
36	chr1:59049800-59051600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr1:59049800-59052800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:59049800-59052800	Enhancers	Ovary	ovary
39	chr1:59050000-59050600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr1:59050000-59050600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr1:59050000-59050600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:59050000-59050600	Flanking Active TSS	A549	lung
43	chr1:59050000-59051800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:59050200-59050800	Enhancers	Duodenum Mucosa	Duodenum
45	chr1:59050200-59051600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:59050200-59052400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:59050200-59052800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:59050200-59052800	Enhancers	HMEC	breast
49	chr1:59050200-59052800	Enhancers	HSMM	muscle
50	chr1:59050200-59053000	Enhancers	HUVEC	blood vessel

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