Variant report

Variant	rs1823221
Chromosome Location	chr3:143544418-143544419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10513219	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11710427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11917152	0.82[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11918501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919227	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2011026	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2361200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55654258	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62268880	0.83[EUR][1000 genomes]
rs62268900	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66585826	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6773298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6794755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6798159	1.00[CEU][hapmap];0.95[CHB][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67981921	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6806661	0.87[CEU][hapmap]
rs72995501	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73158100	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7641634	0.87[CEU][hapmap];0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs7641674	0.81[ASN][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	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:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143536000-143545200	Weak transcription	Gastric	stomach
2	chr3:143539200-143544600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:143539400-143545000	Weak transcription	Liver	Liver
4	chr3:143539600-143546600	Weak transcription	Esophagus	oesophagus
5	chr3:143539600-143550000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:143539800-143558200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:143540000-143549600	Weak transcription	HSMM	muscle
8	chr3:143541000-143554200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:143541400-143544600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:143541400-143545200	Weak transcription	Spleen	Spleen
11	chr3:143541400-143565200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:143541800-143549800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:143542000-143553600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:143542200-143549800	Weak transcription	Brain Anterior Caudate	brain
15	chr3:143542200-143552400	Weak transcription	Brain Angular Gyrus	brain
16	chr3:143542200-143553600	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:143543000-143544800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:143543200-143544600	Enhancers	Brain Substantia Nigra	brain
19	chr3:143543200-143544600	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr3:143543200-143545400	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr3:143543200-143545400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr3:143543200-143545800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr3:143543200-143545800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr3:143543200-143545800	Enhancers	NHDF-Ad	bronchial
25	chr3:143543200-143546200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:143543200-143547800	Enhancers	Colon Smooth Muscle	Colon
27	chr3:143543400-143545200	Weak transcription	Right Atrium	heart
28	chr3:143543400-143545400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:143543400-143545400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:143543400-143545800	Enhancers	Primary B cells from peripheral blood	blood
31	chr3:143543400-143545800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:143543400-143545800	Enhancers	Rectal Smooth Muscle	rectum
33	chr3:143543400-143546000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:143543600-143545000	Enhancers	Dnd41	blood
35	chr3:143543600-143546200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:143543600-143551400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:143543800-143545000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr3:143543800-143545200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:143543800-143545400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr3:143543800-143545400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr3:143543800-143545600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr3:143543800-143545800	Enhancers	Stomach Mucosa	stomach
43	chr3:143544000-143545200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr3:143544000-143545200	Enhancers	Fetal Thymus	thymus
45	chr3:143544000-143545600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:143544000-143546000	Enhancers	Primary B cells from cord blood	blood
47	chr3:143544000-143546000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:143544000-143549800	Weak transcription	Adipose Nuclei	Adipose
49	chr3:143544200-143545000	Enhancers	Primary T cells from cord blood	blood
50	chr3:143544200-143549200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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