Variant report

Variant	rs4839649
Chromosome Location	chr3:143369428-143369429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10513216	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10935500	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1242054	1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs1242057	0.97[ASN][1000 genomes]
rs12629688	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs13059265	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1320916	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1345170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1447741	0.83[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1534162	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs16853999	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16854008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1868174	0.84[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1868175	0.81[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1868177	0.83[ASN][1000 genomes]
rs2121777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4839650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4839651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57630925	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57917966	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58441250	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58652978	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60098452	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60428559	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60633318	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60891486	0.83[ASN][1000 genomes]
rs61645302	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62269851	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62269855	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62269856	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62270560	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6774032	0.83[JPT][hapmap]
rs6774050	0.81[CHB][hapmap]
rs6782154	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs6803893	0.92[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs7629784	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7629855	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7650371	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs7650396	0.84[ASN][1000 genomes]
rs935519	0.83[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs935520	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9831286	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs9844600	0.84[ASN][1000 genomes]
rs9882472	0.93[JPT][hapmap];0.84[ASN][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	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143328200-143376200	Weak transcription	Ovary	ovary
2	chr3:143351600-143369800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:143354200-143373600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:143354200-143374000	Weak transcription	Esophagus	oesophagus
5	chr3:143358400-143371200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:143360200-143369600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:143361400-143373400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:143363400-143371200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:143363400-143372800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:143363400-143373800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:143363400-143373800	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:143363400-143377600	Weak transcription	NHDF-Ad	bronchial
13	chr3:143363600-143375400	Weak transcription	Fetal Thymus	thymus
14	chr3:143363600-143377800	Weak transcription	Adipose Nuclei	Adipose
15	chr3:143363600-143379000	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:143363800-143373800	Weak transcription	HSMMtube	muscle
17	chr3:143364000-143369600	Weak transcription	Fetal Lung	lung
18	chr3:143365200-143370800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:143365800-143371200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:143367400-143390400	Weak transcription	Brain Substantia Nigra	brain
21	chr3:143367600-143373200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:143367600-143375400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:143368000-143369600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:143368200-143370600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:143368200-143370600	Weak transcription	Liver	Liver
26	chr3:143368200-143372600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:143368600-143369600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr3:143368600-143370600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:143368600-143371000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:143368800-143372200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:143369000-143369800	Strong transcription	Primary B cells from cord blood	blood
32	chr3:143369000-143370200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:143369000-143370400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:143369000-143370800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:143369000-143371200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr3:143369000-143371800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:143369200-143370200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:143369400-143370200	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr3:143369400-143370200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:143369400-143370400	Weak transcription	Primary T cells from cord blood	blood
41	chr3:143369400-143374600	Weak transcription	Lung	lung

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