Variant report

Variant	rs10789066
Chromosome Location	chr1:59010904-59010905
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59000333..59003093-chr1:59009787..59012199,2	MCF-7	breast:
2	chr1:58983446..58986008-chr1:59008978..59011103,2	K562	blood:
3	chr1:59004925..59008153-chr1:59009746..59011637,3	MCF-7	breast:
4	chr1:59010701..59012328-chr1:59112006..59114513,3	MCF-7	breast:
5	chr1:59010739..59012349-chr1:59084294..59086117,2	MCF-7	breast:
6	chr1:59010739..59013825-chr1:59014370..59019048,5	K562	blood:
7	chr1:59010376..59013266-chr1:59015138..59019159,5	K562	blood:
8	chr1:59009849..59013755-chr1:59040870..59045611,9	MCF-7	breast:
9	chr1:59010302..59014215-chr1:59041338..59045361,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184292	Chromatin interaction
ENSG00000270209	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10458559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10789064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10789067	0.91[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10889099	0.94[ASN][1000 genomes]
rs10889100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889101	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109895	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207238	0.82[ASN][1000 genomes]
rs11207239	0.82[ASN][1000 genomes]
rs11207245	0.81[ASN][1000 genomes]
rs11207246	0.94[ASN][1000 genomes]
rs11207247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11207248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11207250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207254	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207255	1.00[ASN][1000 genomes]
rs11207260	0.88[ASN][1000 genomes]
rs11207262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11207264	0.81[ASN][1000 genomes]
rs11207265	0.81[ASN][1000 genomes]
rs11207266	0.81[ASN][1000 genomes]
rs11207267	0.81[ASN][1000 genomes]
rs11207268	0.81[ASN][1000 genomes]
rs11581395	0.95[CEU][hapmap]
rs11581594	0.81[ASN][1000 genomes]
rs11582299	0.81[ASN][1000 genomes]
rs11583248	0.81[ASN][1000 genomes]
rs11589214	0.88[ASN][1000 genomes]
rs11589236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11590757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11590785	0.94[ASN][1000 genomes]
rs12030713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12058651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12067296	0.88[ASN][1000 genomes]
rs12067565	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12068196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12068201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12068391	0.88[ASN][1000 genomes]
rs12068457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12068597	0.81[ASN][1000 genomes]
rs12069688	0.81[ASN][1000 genomes]
rs12070503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12072998	0.94[ASN][1000 genomes]
rs12077340	0.88[ASN][1000 genomes]
rs12077766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12080357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12087583	0.84[ASN][1000 genomes]
rs12088905	0.82[ASN][1000 genomes]
rs12092564	0.81[ASN][1000 genomes]
rs12097882	0.88[ASN][1000 genomes]
rs12118488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12121129	0.82[ASN][1000 genomes]
rs12124662	0.95[CEU][hapmap]
rs12125391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133823	0.94[ASN][1000 genomes]
rs12139475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12141238	0.94[ASN][1000 genomes]
rs12142098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12406405	0.84[ASN][1000 genomes]
rs17117742	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17117873	1.00[JPT][hapmap]
rs17117877	0.81[ASN][1000 genomes]
rs17372425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17461345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1775002	0.86[CHB][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2087799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232822	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs232826	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs232841	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs232842	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs232844	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs232847	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs232848	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs232849	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2406784	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34023272	0.88[ASN][1000 genomes]
rs34135541	0.88[ASN][1000 genomes]
rs3893156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3893157	0.81[ASN][1000 genomes]
rs41313363	0.84[ASN][1000 genomes]
rs486463	0.95[CEU][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4912195	0.95[CEU][hapmap]
rs56049576	1.00[ASN][1000 genomes]
rs56087605	0.82[ASN][1000 genomes]
rs56138615	0.82[ASN][1000 genomes]
rs562166	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs584579	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59607787	0.88[ASN][1000 genomes]
rs59924197	0.84[ASN][1000 genomes]
rs602579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603031	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60490291	0.94[ASN][1000 genomes]
rs60726128	1.00[ASN][1000 genomes]
rs61779295	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61779296	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs620342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs627218	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6587819	0.91[CEU][hapmap]
rs6587820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587821	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6587828	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs659061	0.91[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6663327	0.81[ASN][1000 genomes]
rs6666138	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6666304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6679808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6687324	0.95[CEU][hapmap]
rs6690139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6704300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs672359	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67264345	0.81[ASN][1000 genomes]
rs67443104	0.88[ASN][1000 genomes]
rs67639631	0.93[EUR][1000 genomes]
rs67673245	0.81[ASN][1000 genomes]
rs67805407	0.88[ASN][1000 genomes]
rs68192782	0.88[ASN][1000 genomes]
rs72672216	0.94[ASN][1000 genomes]
rs7355165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7355166	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7517424	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7520008	0.93[EUR][1000 genomes]
rs7536230	0.95[CEU][hapmap]
rs7536867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7546900	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547036	0.95[CEU][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7547070	0.84[ASN][1000 genomes]
rs905567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs10789066	TACSTD2	cis	Thyroid	GTEx
rs10789066	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58974800-59011800	Weak transcription	Spleen	Spleen
2	chr1:58977200-59011400	Weak transcription	Ovary	ovary
3	chr1:58977400-59011400	Weak transcription	Left Ventricle	heart
4	chr1:58977400-59011400	Weak transcription	Lung	lung
5	chr1:58977600-59011000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:58979000-59011400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:58990800-59011000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:58994200-59011000	Weak transcription	HSMM	muscle
9	chr1:58996200-59011000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:59001200-59011400	Weak transcription	Pancreas	Pancrea
11	chr1:59001800-59011200	Weak transcription	Right Ventricle	heart
12	chr1:59005000-59011200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:59005800-59011000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:59009200-59011200	Weak transcription	Right Atrium	heart
15	chr1:59009400-59011200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:59009400-59011200	Weak transcription	K562	blood
17	chr1:59009600-59011200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr1:59010200-59011000	Enhancers	Fetal Brain Male	brain
19	chr1:59010200-59011000	Enhancers	Fetal Brain Female	brain
20	chr1:59010200-59011400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:59010400-59011000	Enhancers	Colon Smooth Muscle	Colon
22	chr1:59010400-59011200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr1:59010400-59011200	Enhancers	Fetal Kidney	kidney
24	chr1:59010400-59011400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr1:59010400-59011400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr1:59010600-59011000	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:59010600-59011000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:59010600-59011000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:59010600-59011000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr1:59010600-59011000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:59010600-59011000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:59010600-59011000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:59010600-59011000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:59010600-59011000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:59010600-59011000	Enhancers	Aorta	Aorta
36	chr1:59010600-59011000	Enhancers	Brain Hippocampus Middle	brain
37	chr1:59010600-59011000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr1:59010600-59011000	Enhancers	Stomach Smooth Muscle	stomach
39	chr1:59010600-59011000	Enhancers	HepG2	liver
40	chr1:59010600-59011000	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr1:59010600-59011200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr1:59010600-59011200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:59010600-59011200	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr1:59010600-59011200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:59010600-59011200	Enhancers	Primary T cells from cord blood	blood
46	chr1:59010600-59011200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr1:59010600-59011200	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr1:59010600-59011200	Enhancers	Brain Cingulate Gyrus	brain
49	chr1:59010600-59011200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:59010600-59011200	Enhancers	Fetal Intestine Large	intestine

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