Variant report

Variant	rs6809448
Chromosome Location	chr3:142353730-142353731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11916455	0.94[YRI][hapmap]
rs11917460	0.89[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11928203	0.84[ASW][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs13070239	0.85[ASW][hapmap];0.87[GIH][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap]
rs13071750	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13074153	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13078890	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085261	0.85[ASW][hapmap];0.87[GIH][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap]
rs13091247	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13095394	0.82[AMR][1000 genomes]
rs13099184	0.85[ASW][hapmap];0.87[GIH][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap]
rs2049326	0.89[CHB][hapmap]
rs2140437	0.84[ASW][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2354858	0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34372236	0.83[ASN][1000 genomes]
rs34392719	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4256152	0.85[GIH][hapmap]
rs4582075	0.94[YRI][hapmap]
rs4594656	0.85[AMR][1000 genomes]
rs4683427	0.83[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62278480	0.81[AMR][1000 genomes];0.80[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	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6809448	XRN1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142334000-142357200	Weak transcription	Pancreas	Pancrea
2	chr3:142343400-142366400	Weak transcription	Fetal Intestine Small	intestine
3	chr3:142345200-142353800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:142346200-142354800	Weak transcription	A549	lung
5	chr3:142348800-142364800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:142349800-142356600	Weak transcription	Fetal Brain Male	brain
7	chr3:142352200-142354400	Weak transcription	Rectal Mucosa Donor 31	rectum

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