Variant report

Variant	rs1380405
Chromosome Location	chr12:84902568-84902569
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	chr12:84901925..84902765-chr12:85235880..85236805,3	MCF-7	breast:
2	chr12:84902037..84902829-chr12:85012613..85013509,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10735473	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746318	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10746323	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746324	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779090	0.89[AMR][1000 genomes]
rs10779093	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10779098	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10779104	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10862853	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10862854	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11116339	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11116412	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12304463	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12317420	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12317626	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1380408	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1380411	0.81[ASN][1000 genomes]
rs1380412	0.81[ASN][1000 genomes]
rs1380415	0.81[ASN][1000 genomes]
rs1459606	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459608	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459611	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17011955	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1903190	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2446663	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2446664	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2446665	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2446666	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2468284	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468300	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2468302	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2611288	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2611292	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2730703	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956440	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35965389	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4237881	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs4287367	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4761116	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4761117	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6539845	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7134046	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7299468	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7314018	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7953925	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7955024	0.85[EUR][1000 genomes]
rs7966752	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7980543	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs898298	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs898299	0.83[MEX][hapmap]
rs979879	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs982022	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs982023	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983151	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899363	chr12:84450824-84940345	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv899365	chr12:84511125-84940345	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899369	chr12:84536107-85067814	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1035863	chr12:84710250-85331290	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1035236	chr12:84790507-85350433	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv430521	chr12:84886467-84926332	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv899373	chr12:84891803-84999922	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:84899400-84903200	Enhancers	Fetal Stomach	stomach
2	chr12:84899800-84903400	Enhancers	Adipose Nuclei	Adipose
3	chr12:84901000-84903000	Enhancers	Fetal Muscle Leg	muscle
4	chr12:84901200-84903200	Enhancers	Colon Smooth Muscle	Colon
5	chr12:84901400-84902600	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr12:84901400-84903800	Enhancers	HMEC	breast
7	chr12:84901600-84902800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr12:84901600-84903400	Flanking Active TSS	NHDF-Ad	bronchial
9	chr12:84901600-84903800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:84901800-84902600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:84901800-84902800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:84901800-84903200	Enhancers	Esophagus	oesophagus
13	chr12:84901800-84903400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:84901800-84903800	Enhancers	NHEK	skin
15	chr12:84902000-84902800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:84902000-84902800	Enhancers	Rectal Smooth Muscle	rectum
17	chr12:84902000-84903000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:84902000-84903200	Enhancers	NHLF	lung
19	chr12:84902000-84903400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:84902000-84903400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr12:84902000-84903400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:84902000-84903600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:84902000-84903800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr12:84902200-84903000	Flanking Active TSS	Hela-S3	cervix
25	chr12:84902200-84903200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:84902200-84903200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:84902400-84902600	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr12:84902400-84903000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:84902400-84903200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:84902400-84903200	Enhancers	Fetal Lung	lung

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