Variant report

Variant	rs2409674
Chromosome Location	chr8:10595878-10595879
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10089615	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10097283	0.82[CHB][hapmap]
rs10099021	0.88[CHD][hapmap]
rs10100265	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10105487	0.95[JPT][hapmap]
rs10107180	0.90[CHD][hapmap]
rs10113332	0.88[CHD][hapmap]
rs10481451	0.88[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs1073913	0.83[ASN][1000 genomes]
rs10903330	0.90[JPT][hapmap]
rs1115866	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1124010	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11250073	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs11250074	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11250077	0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs11250078	0.83[JPT][hapmap]
rs11250080	0.85[JPT][hapmap]
rs11993903	0.85[JPT][hapmap]
rs12542888	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs12676417	0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs13276026	0.81[ASN][1000 genomes]
rs1897207	0.81[ASN][1000 genomes]
rs1968400	0.83[ASN][1000 genomes]
rs1968401	0.83[ASN][1000 genomes]
rs2033369	0.82[CHB][hapmap]
rs2116093	0.82[ASN][1000 genomes]
rs2116095	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2409663	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2409669	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2409672	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2409675	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2898248	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs2898251	0.82[ASN][1000 genomes]
rs4240670	0.94[JPT][hapmap]
rs4321967	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4504595	0.89[CEU][hapmap]
rs4840512	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4840513	0.83[ASN][1000 genomes]
rs4840516	0.81[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs4840517	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4841436	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4841437	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4841452	0.83[CEU][hapmap]
rs57076989	0.83[ASN][1000 genomes]
rs6601513	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6601521	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs6601522	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6601523	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs6601525	0.95[CHD][hapmap]
rs6601529	0.90[JPT][hapmap]
rs6601530	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs6984744	0.81[ASN][1000 genomes]
rs6985218	0.85[CHD][hapmap]
rs6989370	0.82[ASN][1000 genomes]
rs6993841	0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs6995692	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs7002117	0.83[ASN][1000 genomes]
rs7002282	0.83[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs7005905	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs718741	0.83[ASN][1000 genomes]
rs718742	0.82[ASN][1000 genomes]
rs752446	0.86[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs765658	0.83[ASN][1000 genomes]
rs7814757	0.84[JPT][hapmap]
rs7826180	0.92[CHD][hapmap]
rs7826189	0.95[CHD][hapmap]
rs7826458	0.90[CHD][hapmap]
rs7834466	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs9329231	0.82[ASN][1000 genomes]
rs9969626	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1015932	chr8:10357101-10597856	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1022582	chr8:10571218-10636162	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv539468	chr8:10571218-10636162	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1026802	chr8:10576444-10754489	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
8	nsv539469	chr8:10576444-10754489	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1017836	chr8:10591801-10803617	Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1034988	chr8:10591801-10804243	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2409674	FAM167A	cis	intralobular white matter	BrainEAC
rs2409674	GATA4	cis	parietal	SCAN
rs2409674	FLJ10661	cis	cerebellum	SCAN
rs2409674	DEFB136	cis	parietal	SCAN
rs2409674	PRSS55	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10594800-10598800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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