Variant report

Variant	rs16854423
Chromosome Location	chr3:143546559-143546560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10433437	0.90[CHB][hapmap]
rs10513230	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10513231	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs10513232	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11920369	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12497227	0.90[CHB][hapmap]
rs1394403	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1504605	0.85[JPT][hapmap]
rs16854404	1.00[EUR][1000 genomes]
rs16854417	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16854421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16854424	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16854463	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16854493	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16854503	0.90[CHB][hapmap]
rs16854525	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs16854803	1.00[EUR][1000 genomes]
rs17275413	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1823220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1900643	0.90[CHB][hapmap]
rs1989180	0.90[CHB][hapmap]
rs2121774	0.98[ASN][1000 genomes]
rs2361199	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2361204	0.90[CHB][hapmap]
rs2361212	1.00[EUR][1000 genomes]
rs4340702	1.00[EUR][1000 genomes]
rs4499593	1.00[MEX][hapmap]
rs4839613	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4839614	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4839659	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4839660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4839661	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4839662	1.00[ASN][1000 genomes]
rs4839663	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4839670	0.90[CHB][hapmap]
rs55904283	0.98[ASN][1000 genomes]
rs56010653	0.98[ASN][1000 genomes]
rs60882025	1.00[EUR][1000 genomes]
rs61014121	1.00[EUR][1000 genomes]
rs62268898	1.00[ASN][1000 genomes]
rs6440202	0.85[JPT][hapmap]
rs6764661	0.90[CHB][hapmap]
rs6765414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6769847	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6776336	0.90[CHB][hapmap]
rs6792031	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6793658	1.00[ASN][1000 genomes]
rs6799226	0.82[JPT][hapmap]
rs6804065	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6807009	1.00[EUR][1000 genomes]
rs721573	1.00[EUR][1000 genomes]
rs72997316	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72997334	0.98[ASN][1000 genomes]
rs73008747	0.81[ASN][1000 genomes]
rs73869029	1.00[EUR][1000 genomes]
rs73869032	1.00[EUR][1000 genomes]
rs7621206	0.90[CHB][hapmap]
rs7651412	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7652644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs924851	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs951594	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs951595	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9822158	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9827103	0.90[CHB][hapmap]
rs9832471	0.90[CHB][hapmap]
rs9844917	0.85[ASN][1000 genomes]
rs9847107	0.90[CHB][hapmap]

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	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
4	nsv1001076	chr3:143513526-143547076	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv536747	chr3:143513526-143547076	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143539600-143546600	Weak transcription	Esophagus	oesophagus
2	chr3:143539600-143550000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:143539800-143558200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:143540000-143549600	Weak transcription	HSMM	muscle
5	chr3:143541000-143554200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:143541400-143565200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:143541800-143549800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:143542000-143553600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:143542200-143549800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:143542200-143552400	Weak transcription	Brain Angular Gyrus	brain
11	chr3:143542200-143553600	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:143543200-143547800	Enhancers	Colon Smooth Muscle	Colon
13	chr3:143543600-143551400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:143544000-143549800	Weak transcription	Adipose Nuclei	Adipose
15	chr3:143544200-143549200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:143544200-143552800	Weak transcription	Fetal Lung	lung
17	chr3:143544400-143549600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:143544800-143549000	Weak transcription	HUVEC	blood vessel
19	chr3:143545000-143546800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:143545000-143548000	Weak transcription	Primary T cells from cord blood	blood
21	chr3:143545000-143549800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:143545400-143549000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:143545400-143549800	Weak transcription	Brain Substantia Nigra	brain
24	chr3:143545400-143550000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:143545400-143550000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:143545400-143550200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:143545400-143550400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:143545400-143550400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:143545400-143558800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:143545600-143548800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:143545600-143565400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:143545800-143548800	Weak transcription	Stomach Mucosa	stomach
33	chr3:143545800-143549000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:143545800-143549000	Weak transcription	GM12878-XiMat	blood
35	chr3:143545800-143549000	Weak transcription	NHDF-Ad	bronchial
36	chr3:143545800-143549400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:143545800-143549800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:143545800-143550000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:143545800-143551000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:143546000-143548800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:143546000-143550200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:143546000-143559000	Weak transcription	Primary B cells from cord blood	blood
43	chr3:143546200-143546800	Enhancers	Rectal Smooth Muscle	rectum
44	chr3:143546200-143547200	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr3:143546200-143548600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:143546200-143549800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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