Variant report

Variant	rs4845743
Chromosome Location	chr1:152184149-152184150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10749669	0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10749670	0.91[JPT][hapmap]
rs10788824	0.86[JPT][hapmap]
rs10888467	0.82[ASN][1000 genomes]
rs10888468	0.80[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	0.91[JPT][hapmap]
rs11583524	0.84[JPT][hapmap]
rs11584340	0.90[JPT][hapmap]
rs11588174	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs12030667	0.81[CHD][hapmap]
rs12032307	0.90[AMR][1000 genomes]
rs12047495	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1353436	0.81[ASN][1000 genomes]
rs1390488	0.91[JPT][hapmap]
rs1390490	0.86[JPT][hapmap]
rs1496045	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1552991	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1552992	0.82[ASN][1000 genomes]
rs1552993	0.82[ASN][1000 genomes]
rs1552995	0.82[ASN][1000 genomes]
rs1552996	0.82[ASN][1000 genomes]
rs17596572	0.89[AMR][1000 genomes]
rs1858480	0.91[JPT][hapmap]
rs2184953	0.85[JPT][hapmap]
rs3120659	0.86[JPT][hapmap]
rs3126091	0.91[JPT][hapmap]
rs4845423	0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs4845425	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4845736	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4845737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845741	0.82[ASN][1000 genomes]
rs4845745	0.91[JPT][hapmap]
rs4845750	0.91[JPT][hapmap]
rs55879323	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6587666	0.91[JPT][hapmap]
rs6666097	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6666382	0.91[JPT][hapmap]
rs7531094	0.82[ASN][1000 genomes]
rs7545406	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7550106	0.91[JPT][hapmap]
rs877776	0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:29)

SNP	Gene	Cis/trans	Tissue	Source
rs4845743	FLG-AS1	cis	Nerve Tibial	GTEx
rs4845743	FLG	cis	Esophagus Muscularis	GTEx
rs4845743	FLG-AS1	cis	Artery Aorta	GTEx
rs4845743	FLG	cis	Thyroid	GTEx
rs4845743	FLG-AS1	cis	Thyroid	GTEx
rs4845743	FLG-AS1	cis	Artery Tibial	GTEx
rs4845743	VPS45	cis	parietal	SCAN
rs4845743	CRNN	cis	cerebellum	SCAN
rs4845743	FLG	cis	Artery Aorta	GTEx
rs4845743	HRNR	cis	lung	GTEx
rs4845743	RORC	cis	parietal	SCAN
rs4845743	FLG	cis	Nerve Tibial	GTEx
rs4845743	HRNR	cis	Artery Tibial	GTEx
rs4845743	HRNR	cis	Nerve Tibial	GTEx
rs4845743	FLG-AS1	cis	lung	GTEx
rs4845743	FLG-AS1	cis	Adipose Subcutaneous	GTEx
rs4845743	FLG	cis	Artery Tibial	GTEx
rs4845743	MRPS21	cis	cerebellum	SCAN
rs4845743	FLG	cis	lung	GTEx
rs4845743	HRNR	cis	Thyroid	GTEx
rs4845743	LOC339400	cis	normal skin	skin_eQTL
rs4845743	HRNR	cis	Stomach	GTEx
rs4845743	HRNR	cis	Esophagus Muscularis	GTEx
rs4845743	FLG-AS1	cis	Muscle Skeletal	GTEx
rs4845743	FLG-AS1	cis	Stomach	GTEx
rs4845743	HRNR	cis	Esophagus Mucosa	GTEx
rs4845743	FLG-AS1	cis	Heart Left Ventricle	GTEx
rs4845743	FLG-AS1	cis	Esophagus Muscularis	GTEx
rs4845743	HRNR	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152178600-152184200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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