Variant report

Variant	rs1196290
Chromosome Location	chr2:182853206-182853207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1196291	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4666573	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv834479	chr2:182738483-182905444	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv3440551	chr2:182832201-182874730	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1196290	PPP1R1C	cis	cerebellum	SCAN
rs1196290	PLEKHA3	cis	parietal	SCAN
rs1196290	FRZB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182843400-182904000	Weak transcription	Thymus	Thymus
2	chr2:182845400-182879000	Weak transcription	Fetal Thymus	thymus
3	chr2:182850600-182853800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:182850600-182853800	Weak transcription	Psoas Muscle	Psoas
5	chr2:182851800-182853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:182852000-182853400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:182852600-182853800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr2:182852800-182853400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:182852800-182853800	Enhancers	Fetal Heart	heart
10	chr2:182853000-182853400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:182853000-182853400	Enhancers	Colon Smooth Muscle	Colon
12	chr2:182853000-182853400	Enhancers	Hela-S3	cervix

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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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