Variant report

Variant	rs12121129
Chromosome Location	chr1:58947098-58947099
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	chr1:58946986..58949777-chr1:58949804..58952885,4	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10458559	0.82[ASN][1000 genomes]
rs10489815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789064	0.82[ASN][1000 genomes]
rs10789066	0.82[ASN][1000 genomes]
rs10889098	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10889099	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10889100	0.82[ASN][1000 genomes]
rs10889101	0.82[ASN][1000 genomes]
rs1109895	0.82[ASN][1000 genomes]
rs1109896	0.82[ASN][1000 genomes]
rs11207238	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207239	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207246	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207247	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207248	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207250	0.82[ASN][1000 genomes]
rs11207251	0.82[ASN][1000 genomes]
rs11207252	0.82[ASN][1000 genomes]
rs11207253	0.82[ASN][1000 genomes]
rs11207254	0.82[ASN][1000 genomes]
rs11207255	0.82[ASN][1000 genomes]
rs11590785	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12058651	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12070503	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12072998	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12077766	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12080357	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12088905	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118488	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125391	0.82[ASN][1000 genomes]
rs12133823	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12139475	0.88[ASN][1000 genomes]
rs12141238	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12142098	0.82[ASN][1000 genomes]
rs12144759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17117742	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2087799	0.82[ASN][1000 genomes]
rs2406784	0.82[ASN][1000 genomes]
rs3087585	0.88[ASN][1000 genomes]
rs56049576	0.82[ASN][1000 genomes]
rs56087605	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138615	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60490291	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60726128	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587820	0.88[ASN][1000 genomes]
rs6587821	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6661832	0.94[ASN][1000 genomes]
rs6679808	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72672216	0.88[ASN][1000 genomes]
rs7355165	0.88[ASN][1000 genomes]
rs7355166	0.88[ASN][1000 genomes]
rs7515056	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7523411	0.85[EUR][1000 genomes]
rs7536867	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7546900	0.82[ASN][1000 genomes]
rs905567	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv829948	chr1:58803681-58971380	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	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
rs12121129	TACSTD2	cis	Whole Blood	GTEx
rs12121129	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	chr1:58918400-58974000	Weak transcription	Spleen	Spleen
2	chr1:58923200-58954200	Weak transcription	Pancreas	Pancrea
3	chr1:58929000-58954600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:58930400-58949400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:58931000-58954200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:58931000-58954600	Weak transcription	Fetal Intestine Large	intestine
7	chr1:58931000-58954800	Weak transcription	Gastric	stomach
8	chr1:58931000-58977000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:58931200-58952600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:58931200-58969400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:58931200-59010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:58931600-58974000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:58932400-58947400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:58932600-58947400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:58932600-58947600	Weak transcription	Dnd41	blood
16	chr1:58932600-58948400	Weak transcription	Fetal Stomach	stomach
17	chr1:58932600-58954600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:58932600-58974200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:58932600-58977000	Weak transcription	HSMMtube	muscle
20	chr1:58932800-58954000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:58932800-58954200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:58932800-58968000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:58933000-58954200	Weak transcription	Fetal Intestine Small	intestine
24	chr1:58933000-58954400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:58933400-58948000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:58933400-58948800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:58933800-58984800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:58934600-58948800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:58934600-58954600	Weak transcription	Esophagus	oesophagus
30	chr1:58934600-58954600	Weak transcription	Lung	lung
31	chr1:58934600-58968000	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:58934600-58974000	Weak transcription	Right Ventricle	heart
33	chr1:58934800-58948800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:58934800-58954200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:58934800-58954800	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:58934800-58967200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:58934800-58969200	Weak transcription	Liver	Liver
38	chr1:58934800-58976600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:58934800-58994000	Weak transcription	HSMM	muscle
40	chr1:58935000-58974000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:58936600-58948800	Weak transcription	Left Ventricle	heart
42	chr1:58942000-58969200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:58942000-58974200	Weak transcription	Brain Substantia Nigra	brain
44	chr1:58942200-58948400	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr1:58942200-58974200	Weak transcription	Fetal Thymus	thymus
46	chr1:58942400-58954600	Weak transcription	Thymus	Thymus
47	chr1:58943200-58949800	Strong transcription	Primary B cells from cord blood	blood
48	chr1:58944400-58947600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr1:58944400-58967800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:58944600-58976000	Weak transcription	Muscle Satellite Cultured Cells	--

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