Variant report

Variant	rs7564660
Chromosome Location	chr2:72555329-72555330
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10188321	1.00[AMR][1000 genomes]
rs10191381	0.92[YRI][hapmap]
rs10205704	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11126366	0.93[YRI][hapmap]
rs13393356	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13394873	0.85[YRI][hapmap]
rs13397728	1.00[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13397743	1.00[MEX][hapmap]
rs13415635	0.92[YRI][hapmap]
rs590345	0.85[YRI][hapmap]
rs6749568	0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7564660	PRRX1	trans	lymphoblastoid	seeQTL
rs7564660	DSC3	trans	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72531200-72594800	Weak transcription	Esophagus	oesophagus
2	chr2:72537200-72567800	Weak transcription	Ovary	ovary
3	chr2:72538600-72567800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:72541600-72561400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:72551400-72561400	Weak transcription	HSMMtube	muscle
6	chr2:72551600-72557600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:72551800-72563400	Weak transcription	Primary T cells from cord blood	blood
8	chr2:72552600-72568600	Weak transcription	Fetal Brain Male	brain
9	chr2:72553000-72563600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:72553200-72557000	Weak transcription	Fetal Brain Female	brain
11	chr2:72553400-72560800	Weak transcription	Adipose Nuclei	Adipose
12	chr2:72553600-72556200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:72553600-72562200	Weak transcription	Left Ventricle	heart
14	chr2:72553600-72576000	Weak transcription	Fetal Heart	heart
15	chr2:72553800-72557200	Weak transcription	Placenta	Placenta
16	chr2:72553800-72594600	Weak transcription	Aorta	Aorta
17	chr2:72554000-72562000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:72554400-72567600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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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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