Variant report

Variant	rs4319308
Chromosome Location	chr1:192600491-192600492
allele	C/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]
rs10127997	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10801138	0.82[CEU][hapmap]
rs12044559	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12759003	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3795617	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3884536	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233424	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59105666	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6658382	0.85[CEU][hapmap];0.81[CHB][hapmap]

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	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv467005	chr1:192549912-192625360	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv548659	chr1:192549912-192625360	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4319308	RGS1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192596200-192602200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:192596400-192601800	Weak transcription	Fetal Intestine Large	intestine
3	chr1:192597000-192605600	Enhancers	Fetal Lung	lung
4	chr1:192597800-192602600	Enhancers	Liver	Liver
5	chr1:192598000-192602000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:192598800-192603200	Weak transcription	Right Ventricle	heart
7	chr1:192599000-192602200	Weak transcription	Fetal Heart	heart
8	chr1:192599000-192608200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:192599600-192601000	Enhancers	Stomach Mucosa	stomach
10	chr1:192599800-192600600	Enhancers	Pancreas	Pancrea
11	chr1:192599800-192600800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:192599800-192600800	Enhancers	HepG2	liver
13	chr1:192600000-192601000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:192600200-192601200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:192600200-192602400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:192600200-192620400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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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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