Variant report

Variant	rs11541780
Chromosome Location	chr10:97373754-97373755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10882623	0.92[EUR][1000 genomes]
rs10882624	0.92[EUR][1000 genomes]
rs10882626	0.92[EUR][1000 genomes]
rs10882627	0.92[EUR][1000 genomes]
rs10882628	0.92[EUR][1000 genomes]
rs10882629	0.92[EUR][1000 genomes]
rs10882630	0.92[EUR][1000 genomes]
rs10882631	0.92[EUR][1000 genomes]
rs10882632	0.92[EUR][1000 genomes]
rs10882633	0.90[EUR][1000 genomes]
rs10882634	0.92[EUR][1000 genomes]
rs10882635	0.90[EUR][1000 genomes]
rs11188366	0.92[EUR][1000 genomes]
rs11188368	0.92[EUR][1000 genomes]
rs11188369	0.92[EUR][1000 genomes]
rs11188370	0.92[EUR][1000 genomes]
rs11188371	0.92[EUR][1000 genomes]
rs11188376	0.92[EUR][1000 genomes]
rs11542152	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12218873	0.92[EUR][1000 genomes]
rs12242866	0.92[EUR][1000 genomes]
rs12242918	0.92[EUR][1000 genomes]
rs12242923	0.92[EUR][1000 genomes]
rs12248661	0.92[EUR][1000 genomes]
rs12250514	0.92[EUR][1000 genomes]
rs12255572	0.92[EUR][1000 genomes]
rs3176887	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3176892	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3176893	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3181116	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181118	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181125	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181127	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35168849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41291572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62625035	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7073436	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7084606	0.92[EUR][1000 genomes]
rs7086374	0.87[EUR][1000 genomes]
rs7097236	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7099430	0.92[EUR][1000 genomes]
rs7099515	0.92[EUR][1000 genomes]
rs7101227	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73325155	0.92[EUR][1000 genomes]
rs73325195	0.92[EUR][1000 genomes]
rs74150947	0.92[EUR][1000 genomes]
rs7896068	0.92[EUR][1000 genomes]
rs7900437	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7903143	0.90[EUR][1000 genomes]
rs7915682	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7919673	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][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	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11541780	TCTN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97364000-97382000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr10:97364000-97409200	Strong transcription	Primary T cells from cord blood	blood
3	chr10:97364000-97411000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr10:97364400-97378600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:97364400-97378600	Strong transcription	Fetal Brain Female	brain
6	chr10:97364400-97378600	Strong transcription	Spleen	Spleen
7	chr10:97364400-97379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr10:97364400-97403200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:97364600-97377400	Strong transcription	Placenta	Placenta
10	chr10:97364600-97378600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr10:97364600-97378600	Strong transcription	Pancreas	Pancrea
12	chr10:97364600-97378800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr10:97364600-97378800	Strong transcription	NH-A	brain
14	chr10:97364600-97379000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:97364600-97379000	Strong transcription	GM12878-XiMat	blood
16	chr10:97364600-97388400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr10:97364800-97378600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr10:97364800-97378600	Strong transcription	Gastric	stomach
19	chr10:97364800-97378800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr10:97364800-97378800	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr10:97364800-97378800	Strong transcription	Osteobl	bone
22	chr10:97364800-97379000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr10:97364800-97403400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr10:97364800-97411000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:97365000-97378200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:97365000-97378400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr10:97365000-97378600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:97365000-97378600	Strong transcription	Brain Germinal Matrix	brain
29	chr10:97365000-97378800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:97365000-97378800	Strong transcription	Adipose Nuclei	Adipose
31	chr10:97365000-97379000	Strong transcription	Dnd41	blood
32	chr10:97365000-97403000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr10:97365000-97403400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:97365200-97377800	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr10:97365200-97378600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr10:97365200-97378800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr10:97365200-97378800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr10:97365200-97379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr10:97365200-97379200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr10:97365200-97379200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr10:97365200-97379800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:97365200-97382200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr10:97365400-97376000	Strong transcription	Fetal Thymus	thymus
44	chr10:97365400-97377000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr10:97365400-97378600	Strong transcription	Lung	lung
46	chr10:97365400-97378800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr10:97365400-97378800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr10:97365400-97378800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr10:97365400-97378800	Strong transcription	NHEK	skin
50	chr10:97365400-97379000	Strong transcription	Fetal Muscle Trunk	muscle

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