Variant report

Variant	rs12538688
Chromosome Location	chr7:83364914-83364915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1181364	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1181365	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12540327	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13241482	0.82[ASN][1000 genomes]
rs17158110	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2371877	0.82[ASN][1000 genomes]
rs528921	0.92[AFR][1000 genomes]
rs532597	0.87[AFR][1000 genomes]
rs7785664	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017248	chr7:83189888-83385765	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1017237	chr7:83262951-83423389	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2758122	chr7:83300506-83460112	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2759541	chr7:83300506-83460112	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv888609	chr7:83307600-83403157	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv888610	chr7:83307600-83411926	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv888611	chr7:83318875-83415942	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv888612	chr7:83326808-83408914	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
9	nsv888613	chr7:83331315-83403157	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
10	nsv888614	chr7:83349707-83403157	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
11	nsv888615	chr7:83349707-83415942	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv888616	chr7:83352427-83408914	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
13	nsv888617	chr7:83352427-83479375	Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv888618	chr7:83359224-83415942	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12538688	CACNA2D1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83362200-83367400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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

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