Variant report

Variant	rs12403445
Chromosome Location	chr1:180587560-180587561
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10914054	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11799355	0.85[AFR][1000 genomes]
rs11799662	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807477	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12401315	1.00[CEU][hapmap]
rs12759582	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs34853798	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36022153	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67135271	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12403445	RGS16	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180581800-180600600	Weak transcription	Fetal Heart	heart
2	chr1:180582600-180588000	Enhancers	K562	blood
3	chr1:180586000-180589400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:180586000-180589600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:180586000-180590000	Weak transcription	Osteobl	bone
6	chr1:180586400-180587600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:180586400-180587600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr1:180586400-180587600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:180586600-180587600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:180586600-180587600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:180586600-180587600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:180586600-180587600	Enhancers	Adipose Nuclei	Adipose
13	chr1:180586600-180587600	Enhancers	HUVEC	blood vessel
14	chr1:180586800-180594400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:180587400-180587600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:180587400-180587600	Enhancers	Fetal Lung	lung
17	chr1:180587400-180592800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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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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