Variant report

Variant	rs1979290
Chromosome Location	chr4:89789478-89789479
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10516823	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs11724744	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732471	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737515	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11945494	0.89[CHD][hapmap]
rs13118412	0.85[CHD][hapmap]
rs1379935	0.83[CEU][hapmap]
rs17815912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17816002	0.85[CHD][hapmap]
rs2869964	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56837788	0.82[AMR][1000 genomes]
rs72665823	0.82[AMR][1000 genomes]
rs922026	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];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1979290	FAM13A	cis	parietal	SCAN
rs1979290	CD2BP2	trans	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89771000-89803200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr4:89780800-89800600	Weak transcription	Pancreas	Pancrea
3	chr4:89782400-89801200	Weak transcription	Ovary	ovary
4	chr4:89787400-89801200	Weak transcription	Placenta	Placenta
5	chr4:89788200-89790400	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr4:89788400-89791600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:89789400-89789600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:89789400-89790200	Enhancers	Fetal Intestine Small	intestine

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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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