Variant report

Variant	rs12580909
Chromosome Location	chr12:41222963-41222964
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	chr12:41222882..41225557-chr7:143112465..143114503,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1014167	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1028949	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12578583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578762	0.83[ASN][1000 genomes]
rs12579682	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12581257	0.83[ASN][1000 genomes]
rs12581462	0.89[ASN][1000 genomes]
rs12582450	0.83[ASN][1000 genomes]
rs12582480	0.89[ASN][1000 genomes]
rs12582790	0.83[ASN][1000 genomes]
rs12582806	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12810195	0.83[ASN][1000 genomes]
rs12814216	0.87[ASN][1000 genomes]
rs12824161	0.83[ASN][1000 genomes]
rs34409157	0.83[ASN][1000 genomes]
rs34435345	0.83[ASN][1000 genomes]
rs34480545	0.86[ASN][1000 genomes]
rs34588792	0.83[ASN][1000 genomes]
rs35067046	0.83[ASN][1000 genomes]
rs35640051	0.83[ASN][1000 genomes]
rs35840550	0.83[ASN][1000 genomes]
rs56928815	0.83[ASN][1000 genomes]
rs59969287	0.83[ASN][1000 genomes]
rs7303594	0.83[ASN][1000 genomes]
rs7307211	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310770	0.83[ASN][1000 genomes]
rs7311456	0.83[ASN][1000 genomes]
rs73118754	0.83[ASN][1000 genomes]
rs73118756	0.83[ASN][1000 genomes]
rs7312428	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7314477	0.83[ASN][1000 genomes]
rs7960431	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7969238	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	nsv427909	chr12:41054306-41322257	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv832379	chr12:41054440-41232749	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv832380	chr12:41132306-41323961	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3435443	chr12:41206734-41222972	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41214000-41223200	Weak transcription	NHEK	skin
2	chr12:41219400-41223400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:41220000-41223400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:41220600-41223400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:41221400-41224000	Active TSS	Brain Cingulate Gyrus	brain
6	chr12:41221400-41224000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr12:41221400-41224000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:41221600-41224000	Enhancers	HMEC	breast
9	chr12:41221800-41224600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:41222200-41223000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr12:41222200-41223000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr12:41222400-41224000	Active TSS	Brain Hippocampus Middle	brain
13	chr12:41222400-41224000	Active TSS	Fetal Brain Female	brain
14	chr12:41222600-41223600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:41222600-41223600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:41222600-41223800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:41222600-41224200	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr12:41222800-41223200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:41222800-41223400	Enhancers	A549	lung
20	chr12:41222800-41223800	Weak transcription	Brain Anterior Caudate	brain
21	chr12:41222800-41228000	Weak transcription	Fetal Brain Male	brain

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