Variant report

Variant	rs59577561
Chromosome Location	chr12:41401773-41401774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17128992	1.00[EUR][1000 genomes]
rs17553124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2897154	1.00[AFR][1000 genomes]
rs66468524	1.00[EUR][1000 genomes]
rs73111376	1.00[EUR][1000 genomes]
rs73116971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73116979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73116981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73116984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73116988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73126511	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv832382	chr12:41359550-41489681	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1042296	chr12:41372512-41401840	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	nsv427910	chr12:41374913-41650593	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv428587	chr12:41375635-41546845	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59577561	NPAL2	trans	lymphoblastoid	RTeQTL
rs59577561	ARPC2	trans	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41374600-41404800	Weak transcription	Brain Angular Gyrus	brain
2	chr12:41395000-41405200	Weak transcription	Ovary	ovary
3	chr12:41398600-41402000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:41398600-41403600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:41399000-41404400	Weak transcription	Aorta	Aorta
6	chr12:41399000-41404800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:41399200-41404200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:41399800-41402000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:41401400-41403200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:41401400-41406200	ZNF genes & repeats	Fetal Lung	lung

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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