Variant report

Variant	rs11590785
Chromosome Location	chr1:58991470-58991471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:58990533..58993683-chr1:59038930..59041030,3	MCF-7	breast:
2	chr1:58989809..58991764-chr1:59011024..59013989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173406	Chromatin interaction
ENSG00000162600	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10458559	0.94[ASN][1000 genomes]
rs10489815	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10789064	0.94[ASN][1000 genomes]
rs10789065	0.91[ASN][1000 genomes]
rs10789066	0.94[ASN][1000 genomes]
rs10889098	0.81[EUR][1000 genomes]
rs10889099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889100	0.94[ASN][1000 genomes]
rs10889101	0.94[ASN][1000 genomes]
rs10889104	0.83[EUR][1000 genomes]
rs1109895	0.94[ASN][1000 genomes]
rs1109896	0.94[ASN][1000 genomes]
rs11207238	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207239	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207245	0.81[ASN][1000 genomes]
rs11207246	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207247	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207248	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207250	0.94[ASN][1000 genomes]
rs11207251	0.94[ASN][1000 genomes]
rs11207252	0.94[ASN][1000 genomes]
rs11207253	0.94[ASN][1000 genomes]
rs11207254	0.94[ASN][1000 genomes]
rs11207255	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207260	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11207262	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11207264	0.82[EUR][1000 genomes]
rs11207265	0.83[EUR][1000 genomes]
rs11207266	0.83[EUR][1000 genomes]
rs11207267	0.83[EUR][1000 genomes]
rs11207268	0.83[EUR][1000 genomes]
rs11581594	0.83[EUR][1000 genomes]
rs11582299	0.83[EUR][1000 genomes]
rs11583248	0.83[EUR][1000 genomes]
rs11589214	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11589236	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11590757	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12058651	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12067296	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12067565	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12068201	0.83[EUR][1000 genomes]
rs12068391	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12068457	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12068597	0.83[EUR][1000 genomes]
rs12069688	0.83[EUR][1000 genomes]
rs12070503	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12072998	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077340	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12077766	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080357	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12087583	0.82[EUR][1000 genomes]
rs12088905	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12092564	0.83[EUR][1000 genomes]
rs12097882	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12118488	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12121129	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12125391	0.94[ASN][1000 genomes]
rs12133823	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139475	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141238	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142098	0.94[ASN][1000 genomes]
rs12144759	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12406405	0.82[EUR][1000 genomes]
rs17117742	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17117873	0.83[EUR][1000 genomes]
rs17117877	0.83[EUR][1000 genomes]
rs2087799	0.94[ASN][1000 genomes]
rs232848	0.82[ASN][1000 genomes]
rs232849	0.82[ASN][1000 genomes]
rs2406784	0.94[ASN][1000 genomes]
rs3087585	1.00[ASN][1000 genomes]
rs34023272	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34135541	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3893156	0.83[EUR][1000 genomes]
rs3893157	0.83[EUR][1000 genomes]
rs41313363	0.83[EUR][1000 genomes]
rs56049576	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56087605	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56138615	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs562166	0.82[ASN][1000 genomes]
rs584579	0.82[ASN][1000 genomes]
rs59607787	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59924197	0.82[EUR][1000 genomes]
rs602579	0.82[ASN][1000 genomes]
rs603031	0.82[ASN][1000 genomes]
rs60490291	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60726128	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs620342	0.82[ASN][1000 genomes]
rs627218	0.82[ASN][1000 genomes]
rs6587820	1.00[ASN][1000 genomes]
rs6587821	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6661832	0.82[ASN][1000 genomes]
rs6663327	0.83[EUR][1000 genomes]
rs6666138	0.82[EUR][1000 genomes]
rs6666304	0.83[EUR][1000 genomes]
rs6679808	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690139	0.83[EUR][1000 genomes]
rs6704300	0.83[EUR][1000 genomes]
rs67264345	0.83[EUR][1000 genomes]
rs67443104	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67673245	0.83[EUR][1000 genomes]
rs67805407	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68192782	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72672216	1.00[ASN][1000 genomes]
rs7355165	1.00[ASN][1000 genomes]
rs7355166	1.00[ASN][1000 genomes]
rs7515056	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536867	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546900	0.94[ASN][1000 genomes]
rs7547070	0.83[EUR][1000 genomes]
rs905567	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv998092	chr1:58978327-59002319	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11590785	TACSTD2	cis	Whole Blood	GTEx
rs11590785	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58931200-59010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:58934800-58994000	Weak transcription	HSMM	muscle
3	chr1:58946400-58993800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:58953600-58999200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:58963800-58999000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:58966600-59010600	Weak transcription	Placenta	Placenta
7	chr1:58967600-59010600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:58974800-58991600	Weak transcription	Esophagus	oesophagus
9	chr1:58974800-59005000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:58974800-59010800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:58974800-59011800	Weak transcription	Spleen	Spleen
12	chr1:58975000-59010600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:58975000-59010800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:58977000-58993000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:58977200-58994000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:58977200-59005000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:58977200-59010800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:58977200-59011400	Weak transcription	Ovary	ovary
19	chr1:58977400-58994200	Weak transcription	Fetal Lung	lung
20	chr1:58977400-58994200	Weak transcription	Fetal Thymus	thymus
21	chr1:58977400-58994400	Weak transcription	Thymus	Thymus
22	chr1:58977400-58996200	Weak transcription	Fetal Stomach	stomach
23	chr1:58977400-58999000	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:58977400-59005400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:58977400-59008600	Weak transcription	Brain Anterior Caudate	brain
26	chr1:58977400-59010400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:58977400-59010600	Weak transcription	Aorta	Aorta
28	chr1:58977400-59010600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:58977400-59010600	Weak transcription	Psoas Muscle	Psoas
30	chr1:58977400-59011400	Weak transcription	Left Ventricle	heart
31	chr1:58977400-59011400	Weak transcription	Lung	lung
32	chr1:58977600-59011000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:58978200-59010200	Weak transcription	Dnd41	blood
34	chr1:58978400-58991800	Weak transcription	Fetal Heart	heart
35	chr1:58979000-59005400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:58979000-59011400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:58979200-58993200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:58980400-58997600	Weak transcription	GM12878-XiMat	blood
39	chr1:58980600-58994000	Weak transcription	Fetal Intestine Large	intestine
40	chr1:58982200-58993000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:58982200-59008200	Weak transcription	Brain Substantia Nigra	brain
42	chr1:58982800-58998000	Weak transcription	HSMMtube	muscle
43	chr1:58984200-58991800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr1:58984400-58996400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr1:58984600-58991600	Strong transcription	Primary B cells from cord blood	blood
46	chr1:58984800-58993000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:58985200-59010600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:58985800-59010400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:58985800-59010600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:58987000-58992400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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