Variant report

Variant	rs1283798
Chromosome Location	chr12:22021195-22021196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10841904	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1283802	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1283807	0.81[JPT][hapmap]
rs1352909	0.81[JPT][hapmap]
rs1356368	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1356369	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4148665	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4148667	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs697252	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs704193	0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs704194	0.81[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs704206	0.81[JPT][hapmap]
rs704209	0.81[JPT][hapmap]
rs7958833	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs829066	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[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	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1051073	chr12:21910875-22271209	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv470275	chr12:21938544-22126314	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1847099	chr12:22003544-22035425	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1283798	ABCC9	cis	parietal	SCAN
rs1283798	SLCO1B3	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21973800-22025400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:21995600-22022200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:21995600-22034800	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:21995800-22022600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:22003400-22026600	Weak transcription	Psoas Muscle	Psoas
6	chr12:22003600-22022400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:22007800-22022200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:22012200-22026400	Weak transcription	Fetal Heart	heart
9	chr12:22014800-22034800	Weak transcription	Ovary	ovary
10	chr12:22015200-22022200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:22015800-22022200	Weak transcription	Adipose Nuclei	Adipose
12	chr12:22015800-22023200	Weak transcription	Left Ventricle	heart
13	chr12:22016000-22022400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:22016000-22023200	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:22017000-22022200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:22020400-22021200	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr12:22020600-22021200	Enhancers	Liver	Liver
18	chr12:22020800-22021200	Enhancers	Fetal Lung	lung

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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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