Variant report

Variant	rs9588307
Chromosome Location	chr13:111605617-111605618
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11616301	0.92[ASN][1000 genomes]
rs11619139	0.92[ASN][1000 genomes]
rs34492577	0.81[ASN][1000 genomes]
rs4500581	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6492328	0.86[JPT][hapmap]
rs7139802	0.94[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7998604	0.90[ASN][1000 genomes]
rs9583555	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
2	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
3	nsv1050379	chr13:111516429-111701302	Genic enhancers Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv541927	chr13:111516429-111701302	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv456121	chr13:111583422-111660113	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv563162	chr13:111583422-111660113	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv563164	chr13:111595399-111625091	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1045197	chr13:111596127-111642187	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1048206	chr13:111596127-111651763	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1037826	chr13:111596401-111639765	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1045417	chr13:111603363-111642187	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv976152	chr13:111604319-111609360	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9588307	PCID2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111597200-111606400	Weak transcription	NHLF	lung
2	chr13:111598800-111606200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:111598800-111607400	Weak transcription	Right Ventricle	heart
4	chr13:111603200-111605800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:111604000-111607000	Weak transcription	Fetal Muscle Leg	muscle
6	chr13:111604200-111606000	Enhancers	HMEC	breast
7	chr13:111604200-111607000	Weak transcription	Hela-S3	cervix
8	chr13:111604400-111607000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:111604600-111610200	Enhancers	Placenta	Placenta
10	chr13:111605000-111606800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr13:111605200-111607200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr13:111605400-111606600	Weak transcription	Stomach Mucosa	stomach
13	chr13:111605400-111606800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr13:111605400-111608000	Enhancers	Fetal Muscle Trunk	muscle
15	chr13:111605600-111606600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr13:111605600-111606800	Weak transcription	K562	blood
17	chr13:111605600-111607200	Weak transcription	NHEK	skin
18	chr13:111605600-111609600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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