Variant report

Variant	rs998807
Chromosome Location	chr3:115914897-115914898
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10511355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12631840	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12631903	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13078076	0.88[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs1461114	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1461116	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs1461132	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1461134	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1468001	0.97[ASN][1000 genomes]
rs1468003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1947689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2864074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2864075	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4831123	1.00[CEU][hapmap]
rs56138725	0.94[ASN][1000 genomes]
rs6438299	0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs6438300	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap]
rs6438303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438304	0.88[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];0.85[YRI][hapmap]
rs6792060	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6807792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618443	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7629590	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs7638493	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7641198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9812548	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs9818695	0.88[CHB][hapmap]
rs9826725	0.94[ASN][1000 genomes]
rs9834017	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9834315	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9834589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835757	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs9870541	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs9875609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs998806	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2755046	chr3:115818840-115942952	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs998807	TIGIT	cis	parietal	SCAN
rs998807	KIAA2018	cis	parietal	SCAN
rs998807	GOLGB1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115907400-115916400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:115907800-115919800	Weak transcription	Brain Angular Gyrus	brain
3	chr3:115911400-115916800	Weak transcription	Brain Anterior Caudate	brain
4	chr3:115911400-115919400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:115911400-115919400	Weak transcription	Brain Substantia Nigra	brain
6	chr3:115912800-115919600	Weak transcription	Brain Cingulate Gyrus	brain

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