Variant report

Variant	rs12487925
Chromosome Location	chr3:133919238-133919239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10804626	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10804627	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10804628	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10804629	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935098	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10935099	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935100	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935101	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935102	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10935105	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11914721	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11922210	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11925021	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927316	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12485592	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486035	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487646	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12488092	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12488358	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12491300	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12493904	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494030	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12494042	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12631354	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638802	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs14533	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28648514	0.87[ASN][1000 genomes]
rs28883962	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28898351	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36077421	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4077106	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4077108	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4286404	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4286405	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4295144	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4349494	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4450813	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4453837	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4453838	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4505670	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588357	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58480012	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58703957	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59391701	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59839641	0.86[ASN][1000 genomes]
rs60202549	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60326170	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60545528	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60564425	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6439467	0.96[ASN][1000 genomes]
rs6439470	0.87[ASN][1000 genomes]
rs6776195	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6776260	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783989	0.95[ASN][1000 genomes]
rs6791361	0.87[ASN][1000 genomes]
rs6800612	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7432230	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7616326	0.87[ASN][1000 genomes]
rs7626278	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7631521	0.94[ASN][1000 genomes]
rs7646388	0.82[ASN][1000 genomes]
rs9883217	0.87[ASN][1000 genomes]
rs9884008	0.87[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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133874400-133929400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:133874600-133933600	Weak transcription	Colonic Mucosa	Colon
3	chr3:133877600-133935200	Weak transcription	Psoas Muscle	Psoas
4	chr3:133877800-133920200	Weak transcription	Brain Substantia Nigra	brain
5	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
6	chr3:133885600-133919600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:133888400-133923600	Weak transcription	Fetal Heart	heart
8	chr3:133894800-133935200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:133894800-133946800	Weak transcription	Pancreas	Pancrea
10	chr3:133895000-133950000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:133895000-133950200	Weak transcription	Gastric	stomach
12	chr3:133895200-133919600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:133895200-133927200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:133895600-133942800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:133895800-133923400	Weak transcription	Lung	lung
16	chr3:133898600-133919400	Weak transcription	A549	lung
17	chr3:133902000-133919600	Weak transcription	Fetal Brain Male	brain
18	chr3:133902000-133930400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:133902800-133919600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:133903000-133929000	Weak transcription	GM12878-XiMat	blood
21	chr3:133907800-133927400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:133908000-133919400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:133909200-133920400	Weak transcription	Brain Angular Gyrus	brain
24	chr3:133909200-133943000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:133909400-133919600	Weak transcription	Fetal Kidney	kidney
26	chr3:133910600-133919400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:133911600-133929600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr3:133911600-133929800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:133913000-133919800	Weak transcription	NHDF-Ad	bronchial
30	chr3:133913800-133919600	Weak transcription	Hela-S3	cervix
31	chr3:133914000-133919800	Weak transcription	HUVEC	blood vessel
32	chr3:133914600-133919600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:133916200-133919400	Weak transcription	Dnd41	blood
34	chr3:133916200-133919400	Weak transcription	NH-A	brain
35	chr3:133916200-133920200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:133916600-133919400	Weak transcription	HepG2	liver
37	chr3:133917200-133919800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:133917200-133920400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:133917400-133919600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:133917400-133919600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:133917400-133919800	Strong transcription	Esophagus	oesophagus
42	chr3:133917400-133921600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr3:133917400-133921800	Strong transcription	Liver	Liver
44	chr3:133917400-133921800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:133917400-133922000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:133917400-133922400	Strong transcription	Primary B cells from cord blood	blood
47	chr3:133917800-133919600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:133917800-133919800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:133917800-133920800	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:133917800-133920800	Strong transcription	Thymus	Thymus

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