Variant report

Variant	rs11207237
Chromosome Location	chr1:58940320-58940321
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10789063	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10789067	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10889098	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1114660	0.96[ASN][1000 genomes]
rs11207236	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207240	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207245	0.82[AMR][1000 genomes]
rs1121422	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11581395	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12030713	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12088149	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124662	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388981	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1775002	0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs232826	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs28529311	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087585	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs338224	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338225	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338228	0.94[AFR][1000 genomes]
rs486463	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4912195	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4912344	0.83[ASN][1000 genomes]
rs6587818	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587819	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587820	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587828	0.83[ASN][1000 genomes]
rs659061	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6656025	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6661832	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6667614	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6667703	0.88[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6687324	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67639631	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7517424	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7520008	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7536230	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544032	0.83[ASN][1000 genomes]
rs7547036	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7554278	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660901	0.89[CHB][hapmap];1.00[JPT][hapmap];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
rs11207237	TACSTD2	cis	Thyroid	GTEx
rs11207237	TACSTD2	cis	Whole Blood	GTEx
rs11207237	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 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	chr1:58925000-58942400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:58926400-58942800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:58927400-58943200	Weak transcription	Primary B cells from cord blood	blood
6	chr1:58928600-58945800	Weak transcription	Aorta	Aorta
7	chr1:58929000-58954600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:58930400-58945800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:58930400-58949400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:58931000-58954200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:58931000-58954600	Weak transcription	Fetal Intestine Large	intestine
12	chr1:58931000-58954800	Weak transcription	Gastric	stomach
13	chr1:58931000-58977000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:58931200-58952600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:58931200-58969400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:58931200-59010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:58931600-58974000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:58932200-58945800	Weak transcription	Adipose Nuclei	Adipose
19	chr1:58932400-58947400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:58932600-58946000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:58932600-58947400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:58932600-58947600	Weak transcription	Dnd41	blood
23	chr1:58932600-58948400	Weak transcription	Fetal Stomach	stomach
24	chr1:58932600-58954600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:58932600-58974200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:58932600-58977000	Weak transcription	HSMMtube	muscle
27	chr1:58932800-58954000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:58932800-58954200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:58932800-58968000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:58933000-58943200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:58933000-58945800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:58933000-58954200	Weak transcription	Fetal Intestine Small	intestine
33	chr1:58933000-58954400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:58933400-58948000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:58933400-58948800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:58933800-58984800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:58934600-58948800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:58934600-58954600	Weak transcription	Esophagus	oesophagus
39	chr1:58934600-58954600	Weak transcription	Lung	lung
40	chr1:58934600-58968000	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:58934600-58974000	Weak transcription	Right Ventricle	heart
42	chr1:58934800-58942600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:58934800-58945000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:58934800-58945200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:58934800-58945200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:58934800-58945800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:58934800-58945800	Weak transcription	Ovary	ovary
48	chr1:58934800-58948800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:58934800-58954200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:58934800-58954800	Weak transcription	Fetal Muscle Leg	muscle

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