Variant report

Variant	rs3766142
Chromosome Location	chr1:169800400-169800401
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10733054	0.81[EUR][1000 genomes]
rs10737549	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10737550	0.95[ASN][1000 genomes]
rs10737551	0.92[ASN][1000 genomes]
rs10800479	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800480	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800481	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10800483	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10800484	0.94[ASN][1000 genomes]
rs10800485	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10800486	0.95[EUR][1000 genomes]
rs10919239	0.81[EUR][1000 genomes]
rs10919245	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919248	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919251	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10919257	0.95[ASN][1000 genomes]
rs10919263	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12133843	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883436	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2056981	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2179396	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2205851	0.81[EUR][1000 genomes]
rs2281039	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294322	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294496	0.95[ASN][1000 genomes]
rs2420512	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420514	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2491087	0.85[EUR][1000 genomes]
rs2806386	0.83[EUR][1000 genomes]
rs2901179	0.95[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3753308	0.91[EUR][1000 genomes]
rs3766132	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766134	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766137	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766144	0.94[ASN][1000 genomes]
rs3766148	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766151	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766154	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4376791	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508080	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4614317	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4615900	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656196	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656197	0.95[ASN][1000 genomes]
rs4656199	0.95[ASN][1000 genomes]
rs4656200	0.95[ASN][1000 genomes]
rs4656721	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656724	0.95[ASN][1000 genomes]
rs4656725	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6427217	0.81[EUR][1000 genomes]
rs6427220	0.90[ASN][1000 genomes]
rs6427224	0.95[ASN][1000 genomes]
rs6427225	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6427226	0.89[ASN][1000 genomes]
rs6427227	0.90[ASN][1000 genomes]
rs6427228	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6656965	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6664099	0.95[ASN][1000 genomes]
rs6668114	0.88[ASN][1000 genomes]
rs6669794	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6670818	0.91[EUR][1000 genomes]
rs6671752	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6676810	0.81[EUR][1000 genomes]
rs6680508	0.81[EUR][1000 genomes]
rs6680650	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680938	0.87[ASN][1000 genomes]
rs6682137	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6682835	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6683056	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6684481	0.95[ASN][1000 genomes]
rs6687377	0.93[ASN][1000 genomes]
rs6702969	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs717481	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732185	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7519364	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7525259	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526261	0.81[EUR][1000 genomes]
rs7530237	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545011	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9287097	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3766142	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs3766142	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169764800-169818200	Weak transcription	Esophagus	oesophagus
2	chr1:169764800-169818200	Weak transcription	Lung	lung
3	chr1:169764800-169823600	Weak transcription	Gastric	stomach
4	chr1:169765000-169808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:169765000-169821800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:169765200-169802000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:169765200-169807800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:169765200-169808000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:169765200-169809000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:169765200-169814800	Weak transcription	Brain Anterior Caudate	brain
11	chr1:169765200-169815200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:169765200-169818800	Weak transcription	Brain Angular Gyrus	brain
13	chr1:169765200-169820600	Weak transcription	Psoas Muscle	Psoas
14	chr1:169765200-169823400	Weak transcription	Right Ventricle	heart
15	chr1:169765400-169808000	Weak transcription	Fetal Heart	heart
16	chr1:169765400-169822600	Weak transcription	Colonic Mucosa	Colon
17	chr1:169765600-169808000	Weak transcription	Small Intestine	intestine
18	chr1:169765600-169818200	Weak transcription	NHLF	lung
19	chr1:169765800-169808000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:169765800-169815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:169765800-169818400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:169773400-169808000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:169774800-169800800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:169776400-169808000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:169777400-169815400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:169784000-169814000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:169784000-169814800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:169786400-169801400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:169786600-169841400	Strong transcription	Dnd41	blood
31	chr1:169788600-169823600	Weak transcription	Pancreas	Pancrea
32	chr1:169789000-169801800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:169789200-169818600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:169790400-169808000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:169790800-169803200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:169790800-169804600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:169790800-169808000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:169790800-169808800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:169791000-169804600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:169791200-169802800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr1:169791200-169803000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:169791200-169804200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:169791200-169808800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:169791200-169810800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:169791200-169841200	Strong transcription	Fetal Thymus	thymus
46	chr1:169792400-169800800	Weak transcription	Fetal Stomach	stomach
47	chr1:169793200-169802200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr1:169793800-169800800	Weak transcription	Thymus	Thymus
49	chr1:169793800-169808000	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:169793800-169808000	Weak transcription	Fetal Brain Male	brain

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