Variant report

Variant	rs2049969
Chromosome Location	chr20:41089079-41089080
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10485694	1.00[ASN][1000 genomes]
rs11904854	1.00[ASN][1000 genomes]
rs11906033	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11907808	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1467394	1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs35041089	1.00[ASN][1000 genomes]
rs35324452	1.00[ASN][1000 genomes]
rs35762999	1.00[ASN][1000 genomes]
rs35800638	1.00[ASN][1000 genomes]
rs4812596	1.00[MEX][hapmap]
rs57772475	1.00[ASN][1000 genomes]
rs57920496	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6016806	1.00[ASN][1000 genomes]
rs6016807	1.00[ASN][1000 genomes]
rs6016808	1.00[ASN][1000 genomes]
rs6016809	1.00[ASN][1000 genomes]
rs6016810	1.00[ASN][1000 genomes]
rs6016813	1.00[ASN][1000 genomes]
rs6030273	1.00[ASN][1000 genomes]
rs6030274	1.00[ASN][1000 genomes]
rs6030275	1.00[ASN][1000 genomes]
rs6030276	1.00[ASN][1000 genomes]
rs6030277	1.00[ASN][1000 genomes]
rs6030282	1.00[ASN][1000 genomes]
rs6030286	1.00[ASN][1000 genomes]
rs6030289	1.00[ASN][1000 genomes]
rs6093659	1.00[ASN][1000 genomes]
rs6093660	1.00[ASN][1000 genomes]
rs6102825	1.00[ASN][1000 genomes]
rs6102855	1.00[ASN][1000 genomes]
rs6102856	1.00[ASN][1000 genomes]
rs6102859	1.00[ASN][1000 genomes]
rs6102860	1.00[ASN][1000 genomes]
rs6102863	1.00[ASN][1000 genomes]
rs6102870	1.00[ASN][1000 genomes]
rs6102871	1.00[ASN][1000 genomes]
rs7263792	1.00[ASN][1000 genomes]
rs73271582	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73271583	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73273400	1.00[ASN][1000 genomes]
rs73908945	1.00[ASN][1000 genomes]
rs8118149	1.00[ASN][1000 genomes]
rs8119002	0.87[CEU][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs8122692	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv833987	chr20:41007663-41184914	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv1059852	chr20:41087948-41217672	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv544276	chr20:41087948-41217672	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2049969	SPINT3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41087200-41089200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:41088800-41089200	Enhancers	Fetal Muscle Leg	muscle
3	chr20:41089000-41089200	Enhancers	Right Atrium	heart
4	chr20:41089000-41089400	Enhancers	Brain Germinal Matrix	brain

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