Variant report

Variant	rs1552991
Chromosome Location	chr1:152165878-152165879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 40 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10749669	0.91[JPT][hapmap]
rs10749670	0.91[JPT][hapmap]
rs10788824	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10888466	0.81[ASN][1000 genomes]
rs10888470	0.91[JPT][hapmap]
rs10888471	0.91[JPT][hapmap]
rs10888473	0.91[JPT][hapmap]
rs11204947	0.91[JPT][hapmap]
rs11204948	0.91[JPT][hapmap]
rs11204980	0.91[JPT][hapmap]
rs11204981	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs11583524	0.84[JPT][hapmap]
rs11584340	0.90[JPT][hapmap]
rs11588174	0.91[JPT][hapmap]
rs12047495	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1390488	0.91[JPT][hapmap]
rs1390490	0.86[JPT][hapmap]
rs1496045	0.91[JPT][hapmap]
rs1858480	0.91[JPT][hapmap]
rs2184953	0.85[JPT][hapmap]
rs3120659	0.86[JPT][hapmap]
rs3126091	0.91[JPT][hapmap]
rs4845423	0.91[JPT][hapmap]
rs4845736	0.91[JPT][hapmap]
rs4845737	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845743	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845745	0.91[JPT][hapmap]
rs4845750	0.91[JPT][hapmap]
rs55879323	0.82[ASN][1000 genomes]
rs6587666	0.91[JPT][hapmap]
rs6666382	0.91[JPT][hapmap]
rs7550106	0.91[JPT][hapmap]
rs877776	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv872442	chr1:152054120-152187641	Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv547854	chr1:152145661-152165878	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:40)

SNP	Gene	Cis/trans	Tissue	Source
rs1552991	LOC339400	cis	putamen	BrainEAC
rs1552991	RORC	cis	parietal	SCAN
rs1552991	LOC339400	cis	inferior olivary nucleus	BrainEAC
rs1552991	HRNR	cis	Stomach	GTEx
rs1552991	MRPS21	cis	cerebellum	SCAN
rs1552991	FLG	cis	Artery Aorta	GTEx
rs1552991	FLG-AS1	cis	Stomach	GTEx
rs1552991	FLG-AS1	cis	Artery Aorta	GTEx
rs1552991	FLG	cis	Thyroid	GTEx
rs1552991	VPS45	cis	parietal	SCAN
rs1552991	LOC339400	cis	substantia nigra	BrainEAC
rs1552991	LOC339400	cis	hippocampus	BrainEAC
rs1552991	FLG	cis	Nerve Tibial	GTEx
rs1552991	FLG-AS1	cis	Heart Left Ventricle	GTEx
rs1552991	LOC339400	cis	temporal cortex	BrainEAC
rs1552991	LOC339400	cis	intralobular white matter	BrainEAC
rs1552991	FLG-AS1	cis	Thyroid	GTEx
rs1552991	FLG-AS1	cis	Nerve Tibial	GTEx
rs1552991	HRNR	cis	Artery Tibial	GTEx
rs1552991	HRNR	cis	Adipose Subcutaneous	GTEx
rs1552991	HRNR	cis	lung	GTEx
rs1552991	FLG	cis	Artery Tibial	GTEx
rs1552991	HRNR	cis	Esophagus Muscularis	GTEx
rs1552991	LOC339400	cis	normal skin	skin_eQTL
rs1552991	FLG-AS1	cis	lung	GTEx
rs1552991	HRNR	cis	Nerve Tibial	GTEx
rs1552991	FLG-AS1	cis	Esophagus Muscularis	GTEx
rs1552991	LOC339400	cis	frontal cortex	BrainEAC
rs1552991	FLG	cis	Esophagus Muscularis	GTEx
rs1552991	HRNR	cis	Thyroid	GTEx
rs1552991	LOC339400	cis	occipital cortex	BrainEAC
rs1552991	FLG-AS1	cis	Muscle Skeletal	GTEx
rs1552991	FLG-AS1	cis	Artery Tibial	GTEx
rs1552991	FLG	cis	lung	GTEx
rs1552991	CRNN	cis	cerebellum	SCAN
rs1552991	HRNR	cis	Esophagus Mucosa	GTEx
rs1552991	FLG-AS1	cis	Adipose Subcutaneous	GTEx
rs1552991	LOC339400	cis	cerebellar cortex	BrainEAC
rs1552991	LOC339400	cis	brain	BrainEAC
rs1552991	FLG	cis	Liver	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152162200-152180200	Weak transcription	Ovary	ovary
2	chr1:152164400-152178400	Weak transcription	Esophagus	oesophagus

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