Variant report

Variant	rs12638802
Chromosome Location	chr3:133890941-133890942
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133880944..133883730-chr3:133890634..133894226,3	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10804626	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804628	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10804629	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935098	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10935099	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935100	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935101	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10935105	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11914721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11927316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485592	1.00[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12486035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12487646	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12487925	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12488092	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12488358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12491300	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12493904	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12494030	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494042	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12631354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs14533	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28648514	0.85[ASN][1000 genomes]
rs28883962	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28898351	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36077421	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4077106	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4077108	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4286404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4286405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4295144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4349494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4450813	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4453837	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4453838	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4505670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4588357	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58480012	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58703957	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59391701	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59839641	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs60202549	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60326170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60545528	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60564425	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439467	0.94[ASN][1000 genomes]
rs6439470	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6439472	1.00[CEU][hapmap]
rs6776195	1.00[CEU][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776260	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783989	0.97[ASN][1000 genomes]
rs6791361	0.85[ASN][1000 genomes]
rs6800612	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616326	0.85[ASN][1000 genomes]
rs7626278	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7631521	0.92[ASN][1000 genomes]
rs7646388	0.80[ASN][1000 genomes]
rs9883217	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9884008	0.85[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133863000-133902200	Weak transcription	GM12878-XiMat	blood
2	chr3:133864200-133899800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:133864600-133892400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:133866200-133898600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:133871800-133919200	Weak transcription	K562	blood
6	chr3:133873400-133891400	Weak transcription	Fetal Brain Female	brain
7	chr3:133873400-133907400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:133873800-133892200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:133874400-133929400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:133874600-133892200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:133874600-133933600	Weak transcription	Colonic Mucosa	Colon
12	chr3:133877600-133907400	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:133877600-133935200	Weak transcription	Psoas Muscle	Psoas
14	chr3:133877800-133894200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:133877800-133894400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:133877800-133894600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:133877800-133920200	Weak transcription	Brain Substantia Nigra	brain
18	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
19	chr3:133878000-133893000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:133878000-133894400	Weak transcription	NHDF-Ad	bronchial
21	chr3:133878200-133891600	Weak transcription	Brain Anterior Caudate	brain
22	chr3:133878200-133892400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:133878200-133892400	Weak transcription	HSMMtube	muscle
24	chr3:133878200-133893400	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:133878200-133901600	Weak transcription	Fetal Brain Male	brain
26	chr3:133878400-133891600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:133878400-133892200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:133878400-133893000	Weak transcription	Hela-S3	cervix
29	chr3:133878400-133894400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:133878400-133907400	Weak transcription	Brain Angular Gyrus	brain
31	chr3:133878600-133892400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:133878600-133893800	Weak transcription	Right Ventricle	heart
33	chr3:133879000-133891600	Weak transcription	Lung	lung
34	chr3:133879000-133891600	Weak transcription	Thymus	Thymus
35	chr3:133879000-133891600	Weak transcription	Spleen	Spleen
36	chr3:133879000-133892400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:133879000-133892800	Weak transcription	Aorta	Aorta
38	chr3:133879000-133894400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:133879000-133894600	Weak transcription	Gastric	stomach
40	chr3:133879200-133891600	Weak transcription	HepG2	liver
41	chr3:133880000-133892400	Weak transcription	NHLF	lung
42	chr3:133881800-133908800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:133882400-133897400	Weak transcription	Fetal Kidney	kidney
44	chr3:133884600-133900000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:133885000-133893600	Weak transcription	Brain Germinal Matrix	brain
46	chr3:133885000-133902400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr3:133885200-133891200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:133885200-133891600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:133885400-133891000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:133885400-133891200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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