Variant report

Variant	rs3180654
Chromosome Location	chr10:116615045-116615046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1046492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510007	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10885613	0.89[AFR][1000 genomes]
rs10885614	0.92[AFR][1000 genomes]
rs11196929	0.83[AFR][1000 genomes]
rs11196930	0.89[AFR][1000 genomes]
rs11196932	0.89[AFR][1000 genomes]
rs11196935	0.84[AFR][1000 genomes]
rs11196936	0.89[AFR][1000 genomes]
rs11196937	0.89[AFR][1000 genomes]
rs11196939	0.89[AFR][1000 genomes]
rs11196941	0.87[AFR][1000 genomes]
rs11196943	0.86[AFR][1000 genomes]
rs11196944	0.88[AFR][1000 genomes]
rs11196945	0.84[AFR][1000 genomes]
rs11196947	0.81[AFR][1000 genomes]
rs11196948	0.85[AFR][1000 genomes]
rs11196950	0.85[AFR][1000 genomes]
rs11196951	0.85[AFR][1000 genomes]
rs11196952	0.87[AFR][1000 genomes]
rs11196953	0.87[AFR][1000 genomes]
rs11818115	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12218498	0.88[AFR][1000 genomes]
rs12415173	0.92[AFR][1000 genomes]
rs12765350	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771956	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12772800	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773943	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775180	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359079	0.87[AFR][1000 genomes]
rs17092497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092542	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17586888	0.83[AFR][1000 genomes]
rs17663670	0.86[AFR][1000 genomes]
rs17721283	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17794346	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966384	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146805	0.86[AFR][1000 genomes]
rs2146806	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420065	0.89[AFR][1000 genomes]
rs2420066	0.89[AFR][1000 genomes]
rs2420067	0.87[AFR][1000 genomes]
rs2420069	0.87[AFR][1000 genomes]
rs34064819	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34187191	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34683721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35010779	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35622181	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628210	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36036948	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089581	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758603	0.87[AFR][1000 genomes]
rs41284358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55711292	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58587374	0.86[AFR][1000 genomes]
rs60820172	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61596353	0.85[AFR][1000 genomes]
rs61867965	0.88[AFR][1000 genomes]
rs61867966	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61867967	1.00[ASN][1000 genomes]
rs61868018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68085797	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072356	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072364	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074729	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075888	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7079877	0.87[AFR][1000 genomes]
rs7093674	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094072	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749649	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895551	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897937	0.89[AFR][1000 genomes]
rs7903663	0.87[AFR][1000 genomes]
rs7904188	0.92[AFR][1000 genomes]
rs7909566	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909657	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914792	0.89[AFR][1000 genomes]
rs7918253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919649	0.92[AFR][1000 genomes]
rs7920216	0.92[AFR][1000 genomes]
rs7923295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181444	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3180654	TRUB1	Cis_1M	lymphoblastoid	RTeQTL
rs3180654	FAM160B1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116583000-116617600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:116583200-116616800	Weak transcription	K562	blood
3	chr10:116589600-116626600	Weak transcription	Stomach Mucosa	stomach
4	chr10:116589600-116640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:116590800-116616600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr10:116590800-116624400	Strong transcription	Dnd41	blood
7	chr10:116590800-116625600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr10:116590800-116626400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr10:116591000-116616000	Strong transcription	Placenta	Placenta
10	chr10:116591000-116619400	Strong transcription	Fetal Muscle Leg	muscle
11	chr10:116591000-116624800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr10:116591000-116626600	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr10:116592400-116625200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr10:116592600-116616600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr10:116593000-116616800	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr10:116595800-116623000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:116596000-116617000	Strong transcription	Adipose Nuclei	Adipose
18	chr10:116600400-116615200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:116600400-116615800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:116602600-116624800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr10:116604800-116627200	Weak transcription	Small Intestine	intestine
22	chr10:116606200-116616000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr10:116606200-116624200	Weak transcription	Gastric	stomach
24	chr10:116606400-116615200	Weak transcription	HMEC	breast
25	chr10:116606600-116619800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr10:116609200-116619000	Weak transcription	Right Ventricle	heart
27	chr10:116609400-116623400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr10:116609600-116615800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr10:116609600-116619000	Weak transcription	Aorta	Aorta
30	chr10:116609600-116634800	Weak transcription	Spleen	Spleen
31	chr10:116609600-116639400	Weak transcription	Pancreas	Pancrea
32	chr10:116609800-116616600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr10:116610000-116615400	Weak transcription	NHEK	skin
34	chr10:116610200-116625000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr10:116610200-116625000	Weak transcription	Colonic Mucosa	Colon
36	chr10:116610200-116625400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:116610200-116625600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr10:116610200-116634600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr10:116610400-116615800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr10:116610400-116617600	Weak transcription	Fetal Brain Male	brain
41	chr10:116610400-116617600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr10:116610400-116628000	Weak transcription	Esophagus	oesophagus
43	chr10:116610600-116615600	Weak transcription	Brain Angular Gyrus	brain
44	chr10:116610600-116628000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr10:116610800-116616600	Weak transcription	Fetal Stomach	stomach
46	chr10:116610800-116619000	Weak transcription	Brain Germinal Matrix	brain
47	chr10:116610800-116619000	Weak transcription	Ovary	ovary
48	chr10:116611000-116615200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr10:116611000-116616600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:116611000-116619000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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