Variant report

Variant	rs6580654
Chromosome Location	chr12:48556626-48556627
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	chr12:48549808..48555740-chr12:48556420..48560606,6	K562	blood:

Variant related genes	Relation type
ENSG00000177981	Chromatin interaction
ENSG00000258051	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10875743	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10875749	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10875753	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10875763	0.81[AMR][1000 genomes]
rs11168408	0.85[EUR][1000 genomes]
rs11168428	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11168441	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12228750	0.81[EUR][1000 genomes]
rs12368659	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12816820	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1476607	0.87[EUR][1000 genomes]
rs2051851	0.80[EUR][1000 genomes]
rs3087716	0.87[AMR][1000 genomes]
rs3997	0.81[EUR][1000 genomes]
rs7139330	0.80[EUR][1000 genomes]
rs7301003	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7486941	0.80[AMR][1000 genomes]
rs8716	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs973398	0.81[EUR][1000 genomes]
rs9971924	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580654	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48552000-48557800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:48554600-48557000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:48554800-48558200	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:48555000-48556800	Weak transcription	Brain Anterior Caudate	brain
5	chr12:48555000-48558200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:48555600-48557200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:48555800-48557000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:48556000-48557200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:48556000-48557200	Weak transcription	K562	blood
10	chr12:48556200-48556800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr12:48556600-48557000	Weak transcription	Psoas Muscle	Psoas
12	chr12:48556600-48557200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr12:48556600-48557400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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