Variant report

Variant	rs4839672
Chromosome Location	chr3:143551893-143551894
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10433436	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11714060	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1319100	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1319101	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1394398	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1394402	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1979911	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1995529	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1995530	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2011290	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2361202	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2361203	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2361205	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2361206	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2361207	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2361208	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2361209	0.94[EUR][1000 genomes]
rs2885193	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2885194	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2885195	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4286430	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4499594	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4839612	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4839671	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4839673	0.94[EUR][1000 genomes]
rs4839674	1.00[CEU][hapmap]
rs6440195	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs6440196	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6768702	0.94[EUR][1000 genomes]
rs6780027	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6782974	1.00[CEU][hapmap]
rs7623477	0.94[EUR][1000 genomes]
rs7627020	0.94[EUR][1000 genomes]
rs7629598	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7645681	0.94[EUR][1000 genomes]
rs9289669	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9824974	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9836851	0.94[EUR][1000 genomes]
rs9870661	1.00[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv3418674	chr3:143457005-143558357	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	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
rs4839672	C14orf143	trans	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143539800-143558200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:143541000-143554200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:143541400-143565200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:143542000-143553600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:143542200-143552400	Weak transcription	Brain Angular Gyrus	brain
6	chr3:143542200-143553600	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:143544200-143552800	Weak transcription	Fetal Lung	lung
8	chr3:143545400-143558800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:143545600-143565400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:143546000-143559000	Weak transcription	Primary B cells from cord blood	blood
11	chr3:143547000-143558200	Weak transcription	Esophagus	oesophagus
12	chr3:143549000-143552800	Enhancers	Colon Smooth Muscle	Colon
13	chr3:143549200-143565200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:143549400-143552400	Weak transcription	Aorta	Aorta
15	chr3:143549400-143565000	Weak transcription	Primary T cells from cord blood	blood
16	chr3:143549800-143552000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:143550000-143552000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:143550000-143558200	Weak transcription	Right Atrium	heart
19	chr3:143550000-143565200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:143550200-143558800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:143550400-143552400	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr3:143550400-143552400	Weak transcription	Ovary	ovary
23	chr3:143550600-143553400	Weak transcription	Brain Anterior Caudate	brain
24	chr3:143550600-143555000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:143550600-143555000	Weak transcription	HSMMtube	muscle
26	chr3:143550600-143558000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:143550800-143554000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:143551200-143558000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:143551400-143555000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:143551400-143561600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:143551400-143563000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:143551400-143565800	Weak transcription	Adipose Nuclei	Adipose
33	chr3:143551600-143558000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:143551600-143559800	Weak transcription	Stomach Mucosa	stomach
35	chr3:143551800-143552200	Weak transcription	Brain Substantia Nigra	brain
36	chr3:143551800-143552600	Enhancers	GM12878-XiMat	blood
37	chr3:143551800-143553600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:143551800-143558000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr3:143551800-143563600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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