Variant report

Variant	rs12054090
Chromosome Location	chr3:119668285-119668286
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	chr3:119643647..119646085-chr3:119668156..119670521,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10433404	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934500	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10934503	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934505	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10934506	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10934507	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11915717	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11917714	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12108149	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12629015	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12630829	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12634476	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12634889	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12635018	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12638973	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1574154	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16830567	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1870931	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1980718	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276707	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2873950	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28831519	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3814057	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3814058	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4340737	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4624596	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4688042	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4688046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688047	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688053	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4688054	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4688059	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56728675	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57939147	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58493895	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58863896	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60235167	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60389731	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs60393216	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62264706	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62264708	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62264714	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62264734	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62264739	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62264742	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62264743	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62264747	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264749	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62266274	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62266277	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62266281	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6773751	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6797459	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808874	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7633279	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7639388	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:119611400-119682200	Weak transcription	HSMMtube	muscle
3	chr3:119629600-119672200	Weak transcription	Fetal Stomach	stomach
4	chr3:119630800-119697400	Weak transcription	Thymus	Thymus
5	chr3:119631000-119717000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:119640600-119672400	Weak transcription	Osteobl	bone
7	chr3:119641000-119681600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:119641000-119681600	Weak transcription	Fetal Intestine Small	intestine
9	chr3:119641000-119694400	Weak transcription	Fetal Lung	lung
10	chr3:119641200-119681200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:119645400-119669600	Weak transcription	Psoas Muscle	Psoas
12	chr3:119650200-119669800	Weak transcription	Liver	Liver
13	chr3:119650400-119669600	Weak transcription	Left Ventricle	heart
14	chr3:119653600-119669600	Weak transcription	Ovary	ovary
15	chr3:119656400-119669400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:119656400-119680600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:119656400-119681200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:119656400-119700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:119656600-119669800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:119656600-119718400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:119658000-119669800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:119658200-119669000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:119658200-119669400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:119658200-119669600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:119658400-119669400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:119658400-119688400	Weak transcription	NHEK	skin
27	chr3:119658400-119688600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:119662000-119684800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:119662400-119700400	Weak transcription	Fetal Intestine Large	intestine
30	chr3:119663200-119669600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:119663600-119669400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:119663600-119681200	Weak transcription	Primary T cells from cord blood	blood
33	chr3:119664000-119669600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:119664000-119695000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:119664200-119668400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:119664200-119674400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:119664600-119673600	Weak transcription	Small Intestine	intestine
38	chr3:119664600-119700200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:119664600-119702400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:119664800-119668800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:119664800-119669600	Weak transcription	Fetal Heart	heart
42	chr3:119665200-119669200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:119665600-119669200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:119665800-119670000	Weak transcription	GM12878-XiMat	blood
45	chr3:119665800-119671000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:119665800-119697400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:119665800-119716800	Weak transcription	HSMM	muscle
48	chr3:119666000-119669600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:119666000-119669600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:119666000-119679800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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