Variant report

Variant	rs12696134
Chromosome Location	chr3:161791399-161791400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1027921	0.80[EUR][1000 genomes]
rs1119974	0.82[EUR][1000 genomes]
rs1397238	0.80[EUR][1000 genomes]
rs1397239	0.80[EUR][1000 genomes]
rs1510346	0.80[EUR][1000 genomes]
rs1813301	0.81[EUR][1000 genomes]
rs2089737	0.81[EUR][1000 genomes]
rs2136712	0.80[EUR][1000 genomes]
rs2175265	0.80[EUR][1000 genomes]
rs4340718	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856668	0.81[EUR][1000 genomes]
rs6789187	0.81[EUR][1000 genomes]
rs6789851	0.81[EUR][1000 genomes]
rs9816747	0.81[EUR][1000 genomes]
rs9819461	0.80[EUR][1000 genomes]
rs9876455	0.81[EUR][1000 genomes]
rs9883680	0.81[EUR][1000 genomes]
rs993596	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
2	nsv460918	chr3:161754109-161791399	Enhancers Weak transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
3	nsv592143	chr3:161754109-161791399	Enhancers Weak transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12696134	SMC4	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161789400-161793400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:161790200-161793000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:161790600-161791400	Enhancers	Brain Anterior Caudate	brain
4	chr3:161790600-161793400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:161790800-161792000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:161791000-161791400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:161791200-161792600	Enhancers	Cortex derived primary cultured neurospheres	brain

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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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