Variant report

Variant	rs6469915
Chromosome Location	chr8:121325670-121325671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:121324471..121327293-chr8:121521096..121522811,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10092516	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10100841	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10103136	0.86[ASN][1000 genomes]
rs1073523	0.87[ASN][1000 genomes]
rs10955967	0.89[ASN][1000 genomes]
rs10955968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11775222	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11781559	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs11781561	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11783320	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs11785760	0.87[ASN][1000 genomes]
rs12676121	0.87[ASN][1000 genomes]
rs12678188	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs12678374	0.90[CHB][hapmap];0.89[ASN][1000 genomes]
rs1319578	0.87[ASN][1000 genomes]
rs1531131	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1563388	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1563389	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1869831	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1869832	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1993390	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1993391	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2100540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2124470	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198748	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2219240	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2219241	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2219242	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2290520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28529014	0.84[ASN][1000 genomes]
rs34829355	0.80[ASN][1000 genomes]
rs4279641	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4871054	0.84[ASN][1000 genomes]
rs4871055	0.92[ASN][1000 genomes]
rs4871056	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4871057	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs57514813	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57553886	0.87[ASN][1000 genomes]
rs6469905	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6469907	0.83[ASN][1000 genomes]
rs6469908	0.80[ASN][1000 genomes]
rs6469909	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6469910	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6469911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469912	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469913	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6469914	0.89[ASN][1000 genomes]
rs6983911	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6985324	0.89[ASN][1000 genomes]
rs6994888	0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs7003797	0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7004015	0.89[ASN][1000 genomes]
rs7004099	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7006048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7006555	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7010688	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7017945	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7341620	0.89[ASN][1000 genomes]
rs7341686	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7814222	0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7817097	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7817682	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7818861	0.87[ASN][1000 genomes]
rs7819160	0.91[CHB][hapmap]
rs7821139	0.86[ASN][1000 genomes]
rs7827901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7829213	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7830625	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7834446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7835757	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7839121	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7841201	0.89[ASN][1000 genomes]
rs7844334	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7844938	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7845246	0.89[ASN][1000 genomes]
rs959370	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891420	chr8:121194900-121561369	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv612112	chr8:121234298-121385167	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv891421	chr8:121292407-121653902	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6469915	NOV	cis	parietal	SCAN
rs6469915	MAL2	cis	parietal	SCAN
rs6469915	SNTB1	cis	parietal	SCAN
rs6469915	SLC30A8	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:121284800-121347800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr8:121293400-121333200	Weak transcription	Fetal Intestine Large	intestine
3	chr8:121310800-121328200	Weak transcription	Fetal Brain Male	brain
4	chr8:121320400-121372600	Weak transcription	Fetal Intestine Small	intestine
5	chr8:121322400-121326800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr8:121322400-121337400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr8:121322800-121326800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr8:121323200-121344800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr8:121323600-121330600	Weak transcription	Aorta	Aorta
10	chr8:121323800-121345800	Weak transcription	Fetal Muscle Leg	muscle
11	chr8:121325200-121327000	Enhancers	Fetal Stomach	stomach
12	chr8:121325200-121334600	Weak transcription	Placenta	Placenta
13	chr8:121325400-121327800	Weak transcription	Fetal Lung	lung
14	chr8:121325600-121326400	Strong transcription	Ovary	ovary
15	chr8:121325600-121326600	Enhancers	Fetal Kidney	kidney

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