Variant report

Variant	rs3101799
Chromosome Location	chr4:22674170-22674171
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12501294	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1478964	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1843485	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2127177	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2219802	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2581964	0.89[EUR][1000 genomes]
rs2581968	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2581969	0.81[EUR][1000 genomes]
rs2581980	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2581991	0.82[ASN][1000 genomes]
rs2581992	0.82[ASN][1000 genomes]
rs2618951	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2618953	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2618960	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2629975	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4697333	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57301753	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]

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	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv829883	chr4:22666326-22842517	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3101799	GPR125	cis	parietal	SCAN
rs3101799	PPARGC1A	cis	parietal	SCAN
rs3101799	LGI2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22663200-22674800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:22670200-22674200	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr4:22670400-22678600	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr4:22670600-22681800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:22672400-22675600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr4:22672600-22675200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr4:22672600-22675200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr4:22672800-22675400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr4:22673600-22674200	Enhancers	Primary B cells from cord blood	blood
10	chr4:22673600-22675200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:22673800-22674600	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr4:22673800-22675000	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr4:22673800-22675200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr4:22673800-22675400	Enhancers	Fetal Thymus	thymus
15	chr4:22673800-22675800	Enhancers	Thymus	Thymus
16	chr4:22674000-22678800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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