Variant report

Variant	rs12665288
Chromosome Location	chr6:163764417-163764418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163762970..163765052-chr6:163833935..163835995,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL078585.1-2	chr6:163761787-163764622	XLOC_005909

Variant related genes	Relation type
ENSG00000270419	Chromatin interaction
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12662020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12664178	0.89[ASN][1000 genomes]
rs12665052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73603780	1.00[EUR][1000 genomes];0.87[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	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1022610	chr6:163591786-163814041	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv605188	chr6:163697439-163772096	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163745200-163767000	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr6:163745600-163773600	Enhancers	Brain Substantia Nigra	brain
3	chr6:163756800-163764800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:163759000-163768400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr6:163759200-163765200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:163760200-163767000	Weak transcription	Esophagus	oesophagus
7	chr6:163760800-163765200	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr6:163760800-163767200	Enhancers	Brain Hippocampus Middle	brain
9	chr6:163760800-163767400	Weak transcription	NH-A	brain
10	chr6:163761400-163767000	Weak transcription	Brain Germinal Matrix	brain
11	chr6:163761400-163767200	Enhancers	Brain Anterior Caudate	brain
12	chr6:163761800-163765200	Enhancers	Fetal Muscle Leg	muscle
13	chr6:163762000-163764600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:163762400-163765000	Enhancers	Left Ventricle	heart
15	chr6:163762400-163765200	Enhancers	Adipose Nuclei	Adipose
16	chr6:163762800-163767000	Weak transcription	Psoas Muscle	Psoas
17	chr6:163763200-163764600	Weak transcription	Lung	lung
18	chr6:163763200-163765000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:163763200-163765000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr6:163763200-163768000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:163763400-163767200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:163763600-163765000	Enhancers	Fetal Heart	heart
23	chr6:163763800-163767400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:163763800-163768000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr6:163764000-163765200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr6:163764000-163767000	Weak transcription	HSMM	muscle
27	chr6:163764000-163767400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:163764000-163768600	Enhancers	Right Ventricle	heart
29	chr6:163764200-163764600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:163764200-163764600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:163764200-163764800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:163764200-163764800	Enhancers	Right Atrium	heart
33	chr6:163764200-163765000	Enhancers	Spleen	Spleen
34	chr6:163764200-163766400	Weak transcription	HSMMtube	muscle
35	chr6:163764200-163767400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:163764400-163764600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr6:163764400-163764800	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr6:163764400-163765000	Enhancers	Liver	Liver
39	chr6:163764400-163765000	Enhancers	Brain Angular Gyrus	brain
40	chr6:163764400-163769400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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