Variant report

Variant	rs4839673
Chromosome Location	chr3:143563812-143563813
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10433436	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11714060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319100	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319101	1.00[EUR][1000 genomes]
rs1394398	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1394402	1.00[EUR][1000 genomes]
rs1979911	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995529	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995530	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2011290	1.00[EUR][1000 genomes]
rs2361202	1.00[EUR][1000 genomes]
rs2361203	0.94[EUR][1000 genomes]
rs2361205	0.94[EUR][1000 genomes]
rs2361206	0.94[EUR][1000 genomes]
rs2361207	0.94[EUR][1000 genomes]
rs2361208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2361209	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2885193	0.94[EUR][1000 genomes]
rs2885194	0.94[EUR][1000 genomes]
rs2885195	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4286430	0.89[EUR][1000 genomes]
rs4499594	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4839612	0.94[EUR][1000 genomes]
rs4839671	0.94[EUR][1000 genomes]
rs4839672	0.94[EUR][1000 genomes]
rs6440196	0.94[EUR][1000 genomes]
rs6768702	1.00[EUR][1000 genomes]
rs6780027	1.00[EUR][1000 genomes]
rs7623477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7627020	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9289669	1.00[EUR][1000 genomes]
rs9824974	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836851	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9870661	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4839673	C14orf143	trans	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143541400-143565200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:143545600-143565400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:143549200-143565200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:143549400-143565000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:143550000-143565200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:143551400-143565800	Weak transcription	Adipose Nuclei	Adipose
7	chr3:143554200-143565800	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:143555400-143564200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:143558400-143566600	Weak transcription	Esophagus	oesophagus
10	chr3:143558600-143566000	Weak transcription	Ovary	ovary
11	chr3:143559800-143565800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:143559800-143566400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:143559800-143566400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:143560200-143564000	Weak transcription	Fetal Lung	lung
15	chr3:143560200-143564400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:143560200-143565200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:143560200-143565800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:143560200-143566600	Weak transcription	Small Intestine	intestine
19	chr3:143561400-143565800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:143561800-143564200	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:143561800-143564400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:143562000-143564400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:143562000-143564800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:143562000-143565800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:143562200-143566600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:143562400-143565200	Enhancers	Brain Hippocampus Middle	brain
27	chr3:143562400-143565800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:143563200-143564000	Active TSS	Placenta	Placenta
29	chr3:143563200-143567600	Active TSS	GM12878-XiMat	blood
30	chr3:143563600-143565800	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:143563600-143565800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr3:143563800-143564000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr3:143563800-143564000	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr3:143563800-143564200	Weak transcription	Primary B cells from cord blood	blood
35	chr3:143563800-143564400	Weak transcription	Fetal Stomach	stomach
36	chr3:143563800-143564600	Active TSS	Brain Anterior Caudate	brain
37	chr3:143563800-143564800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr3:143563800-143565800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr3:143563800-143565800	Enhancers	Brain Cingulate Gyrus	brain
40	chr3:143563800-143565800	Enhancers	Brain Substantia Nigra	brain
41	chr3:143563800-143566400	Enhancers	Primary monocytes fromperipheralblood	blood

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