Variant report

Variant	rs11207240
Chromosome Location	chr1:58950155-58950156
allele	C/G
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:
2	chr1:58949687..58952504-chr1:58961648..58964337,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10789063	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889098	0.96[ASN][1000 genomes]
rs1114660	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11207236	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207237	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207245	0.87[AMR][1000 genomes]
rs1121422	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11581395	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12030713	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12088149	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388981	0.83[ASN][1000 genomes]
rs28529311	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087585	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs338224	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338225	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338228	0.94[AFR][1000 genomes]
rs4912195	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4912344	0.83[ASN][1000 genomes]
rs6587818	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587819	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587820	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6587828	0.83[ASN][1000 genomes]
rs6656025	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6661832	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6667614	0.83[ASN][1000 genomes]
rs6667703	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6687324	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67639631	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7355165	0.81[AMR][1000 genomes]
rs7517424	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7520008	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7536230	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544032	0.83[ASN][1000 genomes]
rs7554278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660901	0.83[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11207240	TACSTD2	cis	Thyroid	GTEx
rs11207240	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs11207240	TACSTD2	cis	Whole Blood	GTEx

Chromatin state (count:76 , 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	chr1:58931000-58954200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:58931000-58954600	Weak transcription	Fetal Intestine Large	intestine
6	chr1:58931000-58954800	Weak transcription	Gastric	stomach
7	chr1:58931000-58977000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:58931200-58952600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:58931200-58969400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:58931200-59010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:58931600-58974000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:58932600-58954600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:58932600-58974200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:58932600-58977000	Weak transcription	HSMMtube	muscle
15	chr1:58932800-58954000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:58932800-58954200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:58932800-58968000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:58933000-58954200	Weak transcription	Fetal Intestine Small	intestine
19	chr1:58933000-58954400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:58933800-58984800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:58934600-58954600	Weak transcription	Esophagus	oesophagus
22	chr1:58934600-58954600	Weak transcription	Lung	lung
23	chr1:58934600-58968000	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:58934600-58974000	Weak transcription	Right Ventricle	heart
25	chr1:58934800-58954200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:58934800-58954800	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:58934800-58967200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:58934800-58969200	Weak transcription	Liver	Liver
29	chr1:58934800-58976600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:58934800-58994000	Weak transcription	HSMM	muscle
31	chr1:58935000-58974000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:58942000-58969200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:58942000-58974200	Weak transcription	Brain Substantia Nigra	brain
34	chr1:58942200-58974200	Weak transcription	Fetal Thymus	thymus
35	chr1:58942400-58954600	Weak transcription	Thymus	Thymus
36	chr1:58944400-58967800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:58944600-58976000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:58944800-58954600	Weak transcription	Fetal Kidney	kidney
39	chr1:58945000-58950800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:58945000-58954600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr1:58945200-58950600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:58945200-58950600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:58945800-58974200	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:58946000-58954400	Weak transcription	Aorta	Aorta
45	chr1:58946000-58955400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:58946200-58962000	Weak transcription	Adipose Nuclei	Adipose
47	chr1:58946200-58967000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:58946200-58974000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:58946200-58977000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:58946200-58979600	Weak transcription	GM12878-XiMat	blood

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