Variant report

Variant	rs41313363
Chromosome Location	chr1:59041655-59041656
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59009849..59013755-chr1:59040870..59045611,9	MCF-7	breast:
2	chr1:59010302..59014215-chr1:59041338..59045361,8	MCF-7	breast:
3	chr1:59039914..59042841-chr1:59125894..59128684,2	MCF-7	breast:
4	chr1:59039784..59042509-chr1:59074910..59077228,3	MCF-7	breast:
5	chr1:59007888..59009563-chr1:59039964..59042756,2	K562	blood:
6	chr1:59003237..59005403-chr1:59039825..59042747,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162600	Chromatin interaction
ENSG00000173406	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10458559	0.84[ASN][1000 genomes]
rs10789064	0.84[ASN][1000 genomes]
rs10789065	0.82[ASN][1000 genomes]
rs10789066	0.84[ASN][1000 genomes]
rs10889099	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10889100	0.84[ASN][1000 genomes]
rs10889101	0.84[ASN][1000 genomes]
rs10889104	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1109895	0.84[ASN][1000 genomes]
rs1109896	0.84[ASN][1000 genomes]
rs11207246	0.81[AFR][1000 genomes]
rs11207248	0.83[EUR][1000 genomes]
rs11207250	0.84[ASN][1000 genomes]
rs11207251	0.84[ASN][1000 genomes]
rs11207252	0.84[ASN][1000 genomes]
rs11207253	0.84[ASN][1000 genomes]
rs11207254	0.84[ASN][1000 genomes]
rs11207255	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11207260	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207262	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207264	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207266	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207267	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207268	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11581594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11582299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11583248	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11584788	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11589214	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11589236	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11590757	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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];0.97[ASN][1000 genomes]
rs12067565	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12068196	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12068201	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12068391	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12068457	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12068597	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12069688	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12077340	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12077766	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12087583	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12092564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12097882	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12125391	0.84[ASN][1000 genomes]
rs12142098	0.84[ASN][1000 genomes]
rs12406405	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568356	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17117742	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17117873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17117877	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17372425	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17461345	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2087799	0.84[ASN][1000 genomes]
rs232841	1.00[ASN][1000 genomes]
rs232842	1.00[ASN][1000 genomes]
rs232844	1.00[ASN][1000 genomes]
rs232847	1.00[ASN][1000 genomes]
rs232848	0.97[ASN][1000 genomes]
rs232849	0.97[ASN][1000 genomes]
rs2406784	0.84[ASN][1000 genomes]
rs34023272	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34135541	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3893156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3893157	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];0.84[ASN][1000 genomes]
rs562166	0.97[ASN][1000 genomes]
rs584579	0.97[ASN][1000 genomes]
rs59607787	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59924197	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602579	0.97[ASN][1000 genomes]
rs603031	0.97[ASN][1000 genomes]
rs60490291	0.81[AFR][1000 genomes]
rs60726128	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61779295	1.00[ASN][1000 genomes]
rs61779296	1.00[ASN][1000 genomes]
rs620342	0.97[ASN][1000 genomes]
rs627218	0.97[ASN][1000 genomes]
rs6663327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664314	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6666138	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6666304	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6679808	0.81[AFR][1000 genomes]
rs6690139	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6704300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67238056	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67264345	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67443104	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67538366	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67673245	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67805407	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68192782	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7546900	0.84[ASN][1000 genomes]
rs7547070	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs905567	0.84[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
rs41313363	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs41313363	TACSTD2	cis	Whole Blood	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59038400-59043600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:59040000-59041800	Active TSS	Pancreas	Pancrea
3	chr1:59040000-59042000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:59040000-59042000	Active TSS	Stomach Mucosa	stomach
5	chr1:59040200-59043400	Active TSS	NHEK	skin
6	chr1:59040200-59043600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:59040600-59042000	Bivalent/Poised TSS	Fetal Stomach	stomach
8	chr1:59040800-59043400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:59040800-59043400	Active TSS	Placenta Amnion	Placenta Amnion
10	chr1:59041000-59041800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr1:59041000-59043200	Active TSS	HMEC	breast
12	chr1:59041200-59041800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
13	chr1:59041200-59042000	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:59041200-59042200	Transcr. at gene 5' and 3'	Esophagus	oesophagus
15	chr1:59041200-59042200	Active TSS	Lung	lung
16	chr1:59041200-59042800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:59041200-59043200	ZNF genes & repeats	GM12878-XiMat	blood
18	chr1:59041200-59044200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
19	chr1:59041400-59041800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
20	chr1:59041400-59041800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr1:59041400-59042200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
22	chr1:59041400-59043000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
23	chr1:59041400-59043200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr1:59041400-59043200	Active TSS	Hela-S3	cervix
25	chr1:59041400-59043400	Bivalent/Poised TSS	Fetal Kidney	kidney
26	chr1:59041400-59043800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr1:59041400-59043800	Bivalent Enhancer	Fetal Heart	heart
28	chr1:59041600-59041800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:59041600-59041800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:59041600-59041800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
31	chr1:59041600-59041800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr1:59041600-59041800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
33	chr1:59041600-59041800	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:59041600-59041800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:59041600-59041800	Bivalent Enhancer	Adipose Nuclei	Adipose
36	chr1:59041600-59042000	Bivalent Enhancer	Colon Smooth Muscle	Colon
37	chr1:59041600-59042200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr1:59041600-59042400	Bivalent/Poised TSS	Fetal Lung	lung
39	chr1:59041600-59043000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:59041600-59043000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr1:59041600-59043200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
42	chr1:59041600-59043200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:59041600-59043200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
44	chr1:59041600-59043200	Bivalent/Poised TSS	Thymus	Thymus
45	chr1:59041600-59043400	Active TSS	HUVEC	blood vessel
46	chr1:59041600-59043600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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