Variant report

Variant	rs10789067
Chromosome Location	chr1:59010948-59010949
allele	A/C
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
ENSG00000270209	Chromatin interaction
ENSG00000184292	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10458559	0.91[CEU][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10789063	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10789064	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10789065	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10789066	0.91[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10889098	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10889100	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10889101	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1109895	0.82[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1109896	0.89[CEU][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1114660	0.83[ASN][1000 genomes]
rs11207236	0.81[EUR][1000 genomes]
rs11207237	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11207250	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11207251	0.91[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11207252	0.91[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11207253	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11207254	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1121422	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11581395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12030713	0.95[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12088149	0.81[EUR][1000 genomes]
rs12124662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12125391	0.91[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12142098	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1388981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1775002	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2087799	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs232822	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs232826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs232827	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs232830	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs232841	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs232842	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs232844	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs232847	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs232848	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs232849	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2406784	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28529311	0.81[EUR][1000 genomes]
rs3087585	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs338225	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3551	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs486463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4912195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4912344	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs525929	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs562166	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs584579	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs602579	0.95[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs603031	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61779295	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61779296	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs620342	0.91[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs627218	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6587818	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6587819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6587820	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs6587828	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs659061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6667614	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6667703	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs6687324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs672359	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67639631	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7355165	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs7355166	0.93[EUR][1000 genomes]
rs7517424	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7520008	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7536230	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544032	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546900	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7547036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs905567	0.91[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9660901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10789067	TACSTD2	cis	Whole Blood	GTEx
rs10789067	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs10789067	TACSTD2	cis	Thyroid	GTEx

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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