Variant report

Variant	rs12491300
Chromosome Location	chr3:133907161-133907162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133906610..133908855-chr3:133910552..133913545,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163785	Chromatin interaction

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

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

rs_ID	r²[population]
rs10804626	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10804627	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10804628	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10804629	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10935098	0.89[ASN][1000 genomes]
rs10935099	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10935100	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10935101	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10935102	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10935105	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11914721	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11922210	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11925021	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11927316	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12485592	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12486035	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12487646	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12487925	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12488092	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12488358	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12493904	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12494030	0.87[ASN][1000 genomes]
rs12494042	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12631354	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12638802	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs14533	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28648514	0.85[ASN][1000 genomes]
rs28883962	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28898351	0.89[ASN][1000 genomes]
rs36077421	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4077106	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4077108	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4286404	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4286405	0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4295144	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4349494	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4450813	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4453837	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4453838	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4505670	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4588357	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58480012	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58703957	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs59391701	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs59839641	0.86[ASN][1000 genomes]
rs60202549	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60326170	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60545528	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60564425	0.94[ASN][1000 genomes]
rs6439467	0.94[ASN][1000 genomes]
rs6439470	0.85[ASN][1000 genomes]
rs6776195	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6776260	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6783989	0.92[ASN][1000 genomes]
rs6791361	0.85[ASN][1000 genomes]
rs6800612	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7432230	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7616326	0.85[ASN][1000 genomes]
rs7626278	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7631521	0.92[ASN][1000 genomes]
rs7646388	0.80[ASN][1000 genomes]
rs9883217	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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133871800-133919200	Weak transcription	K562	blood
2	chr3:133873400-133907400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:133874400-133929400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:133874600-133933600	Weak transcription	Colonic Mucosa	Colon
5	chr3:133877600-133907400	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:133877600-133935200	Weak transcription	Psoas Muscle	Psoas
7	chr3:133877800-133920200	Weak transcription	Brain Substantia Nigra	brain
8	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
9	chr3:133878400-133907400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:133881800-133908800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:133885600-133907400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:133885600-133919600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:133888400-133923600	Weak transcription	Fetal Heart	heart
14	chr3:133893200-133907200	Weak transcription	Brain Anterior Caudate	brain
15	chr3:133893200-133917400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:133894400-133912600	Weak transcription	Fetal Thymus	thymus
17	chr3:133894800-133907200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:133894800-133912600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:133894800-133917800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:133894800-133917800	Weak transcription	Right Ventricle	heart
21	chr3:133894800-133917800	Weak transcription	Thymus	Thymus
22	chr3:133894800-133935200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:133894800-133946800	Weak transcription	Pancreas	Pancrea
24	chr3:133895000-133910600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:133895000-133914400	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:133895000-133917200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:133895000-133917400	Weak transcription	Esophagus	oesophagus
28	chr3:133895000-133917800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:133895000-133918000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:133895000-133918000	Weak transcription	Spleen	Spleen
31	chr3:133895000-133918600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:133895000-133918800	Weak transcription	Aorta	Aorta
33	chr3:133895000-133950000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:133895000-133950200	Weak transcription	Gastric	stomach
35	chr3:133895200-133912400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:133895200-133919600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:133895200-133927200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr3:133895400-133912600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:133895600-133912600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:133895600-133942800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:133895800-133923400	Weak transcription	Lung	lung
42	chr3:133898600-133919400	Weak transcription	A549	lung
43	chr3:133898800-133916600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:133898800-133916800	Weak transcription	NHEK	skin
45	chr3:133899000-133908200	Weak transcription	Ovary	ovary
46	chr3:133899000-133909000	Weak transcription	Fetal Kidney	kidney
47	chr3:133899000-133918000	Weak transcription	HSMMtube	muscle
48	chr3:133899000-133919200	Weak transcription	NHLF	lung
49	chr3:133899200-133908200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:133899200-133912200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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