Variant report

Variant	rs12538120
Chromosome Location	chr7:108363887-108363888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12534347	0.85[AMR][1000 genomes]
rs12536143	0.85[AMR][1000 genomes]
rs12705490	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2188597	0.89[AMR][1000 genomes];0.91[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	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1023651	chr7:108303048-108385180	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1031096	chr7:108334543-108596014	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv888944	chr7:108348785-108433790	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv981780	chr7:108352758-108409711	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12538120	GPR22	cis	parietal	SCAN
rs12538120	SRPK2	cis	parietal	SCAN
rs12538120	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108361600-108364000	Weak transcription	Fetal Muscle Leg	muscle
2	chr7:108363200-108364400	Enhancers	Brain Germinal Matrix	brain
3	chr7:108363200-108366200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:108363600-108364200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr7:108363600-108365000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:108363800-108364200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:108363800-108364200	Enhancers	H9 Cell Line	embryonic stem cell
8	chr7:108363800-108364200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr7:108363800-108364200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:108363800-108364400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:108363800-108364600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:108363800-108365000	Enhancers	H1 Derived Neuronal Progenitor 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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