Variant report

Variant	rs3019916
Chromosome Location	chr8:108061056-108061057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1461996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1462013	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1466403	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1466404	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1903611	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2126362	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2219653	0.85[ASN][1000 genomes]
rs2346901	0.83[ASN][1000 genomes]
rs2346902	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2920094	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920095	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920097	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2927092	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2927094	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2927095	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2927097	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2927100	0.85[ASN][1000 genomes]
rs2927102	0.87[EUR][1000 genomes]
rs2927103	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2927105	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2927106	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2927109	0.85[ASN][1000 genomes]
rs2927110	0.85[ASN][1000 genomes]
rs2927111	0.85[ASN][1000 genomes]
rs2927114	0.85[ASN][1000 genomes]
rs2927115	0.85[ASN][1000 genomes]
rs2927118	0.85[ASN][1000 genomes]
rs2927121	0.85[ASN][1000 genomes]
rs2927150	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2927161	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2927162	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2927166	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2927167	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2927168	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3019909	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3019910	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3019911	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3019912	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019913	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3019914	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019917	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019933	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019939	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3019944	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3019945	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3019946	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3019948	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3019954	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3019956	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3019957	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3019958	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3019959	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3019960	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3019962	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3019965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3019966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3019978	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4410880	0.81[ASN][1000 genomes]
rs4504601	0.85[CEU][hapmap]
rs7842415	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7842583	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs974911	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs974912	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029202	chr8:107796289-108384241	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv539712	chr8:107796289-108384241	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1034210	chr8:107796489-108384102	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv539713	chr8:107796489-108384102	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv529383	chr8:107796490-108368465	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv915821	chr8:107796490-108393008	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv916496	chr8:107813722-108338822	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1028726	chr8:107816841-108392547	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv497805	chr8:107852509-108368371	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1018159	chr8:108007543-108070058	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv3444219	chr8:108049825-108069307	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
12	esv3391198	chr8:108050825-108080952	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3019916	LRP12	cis	parietal	SCAN
rs3019916	TMEM74	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:108058600-108062000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr8:108060800-108061400	Enhancers	Fetal Intestine Large	intestine
3	chr8:108060800-108061800	Enhancers	Fetal Intestine Small	intestine

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