Variant report

Variant	rs12216401
Chromosome Location	chr6:13076881-13076882
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	chr6:13076579..13079092-chr6:13614860..13616733,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261071	Chromatin interaction
ENSG00000225921	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10807388	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1579135	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1937771	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4132046	0.94[ASN][1000 genomes]
rs4292514	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4357136	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4367379	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4432976	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4492189	0.95[ASN][1000 genomes]
rs4580867	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624870	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5002331	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924689	0.95[ASN][1000 genomes]
rs7738606	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748124	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349456	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369759	0.94[ASN][1000 genomes]
rs9369760	0.91[ASN][1000 genomes]
rs9369768	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369779	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9369815	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9381636	0.95[ASN][1000 genomes]
rs9395335	0.95[ASN][1000 genomes]
rs9473285	0.82[ASN][1000 genomes]
rs9473437	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9473486	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[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	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv817350	chr6:12922859-13137655	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv600992	chr6:12961922-13218549	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13059200-13077600	Weak transcription	Lung	lung
2	chr6:13069800-13082200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:13070400-13077800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:13072600-13082200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:13073400-13078400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:13074600-13077000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr6:13075000-13079400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:13075200-13082600	Enhancers	Brain Anterior Caudate	brain
9	chr6:13075400-13077600	Enhancers	Brain Hippocampus Middle	brain
10	chr6:13075400-13079600	Enhancers	Left Ventricle	heart
11	chr6:13075600-13079200	Enhancers	Right Ventricle	heart
12	chr6:13075800-13077000	Enhancers	Fetal Muscle Leg	muscle
13	chr6:13076000-13077000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:13076000-13077000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:13076000-13077600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:13076200-13077000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:13076200-13077000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr6:13076400-13077000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:13076400-13077000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr6:13076400-13077000	Enhancers	Aorta	Aorta
21	chr6:13076400-13077000	Enhancers	Fetal Kidney	kidney
22	chr6:13076400-13077000	Enhancers	Stomach Smooth Muscle	stomach
23	chr6:13076400-13078000	Enhancers	Pancreas	Pancrea
24	chr6:13076600-13077000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:13076600-13077000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:13076600-13077000	Enhancers	Adipose Nuclei	Adipose
27	chr6:13076600-13077000	Flanking Active TSS	Fetal Heart	heart
28	chr6:13076600-13077000	Enhancers	Fetal Lung	lung
29	chr6:13076600-13077600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:13076600-13078800	Enhancers	Right Atrium	heart
31	chr6:13076800-13077000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:13076800-13077000	Enhancers	Brain Cingulate Gyrus	brain
33	chr6:13076800-13078000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:13076800-13078000	Enhancers	Gastric	stomach
35	chr6:13076800-13078800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:13076800-13080400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:13076800-13082000	Weak transcription	Brain Angular Gyrus	brain

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