Variant report

Variant	rs17794346
Chromosome Location	chr10:116643095-116643096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116639834..116644233-chr10:116697414..116700996,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165832	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10444099	1.00[JPT][hapmap]
rs1045657	1.00[JPT][hapmap]
rs1046492	0.92[CEU][hapmap];0.81[GIH][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490908	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510007	0.85[CEU][hapmap];0.87[GIH][hapmap];0.82[EUR][1000 genomes]
rs10885633	1.00[JPT][hapmap]
rs10885634	1.00[JPT][hapmap]
rs10885636	1.00[JPT][hapmap]
rs10885638	1.00[JPT][hapmap]
rs10885639	1.00[JPT][hapmap]
rs11196963	1.00[CHB][hapmap]
rs11196984	1.00[JPT][hapmap]
rs11196996	1.00[JPT][hapmap]
rs11196999	1.00[JPT][hapmap]
rs11197000	1.00[JPT][hapmap]
rs11197007	1.00[JPT][hapmap]
rs11197010	1.00[JPT][hapmap]
rs11197012	1.00[JPT][hapmap]
rs11818115	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12098332	1.00[JPT][hapmap]
rs12265048	1.00[JPT][hapmap]
rs12269261	1.00[JPT][hapmap]
rs12761122	1.00[JPT][hapmap]
rs12764662	1.00[JPT][hapmap]
rs12765350	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771956	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12772800	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773943	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092497	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092542	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721905	1.00[JPT][hapmap]
rs17795212	1.00[JPT][hapmap]
rs1966384	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105001	1.00[JPT][hapmap]
rs2146806	1.00[ASN][1000 genomes]
rs3180654	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34064819	1.00[ASN][1000 genomes]
rs34187191	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683721	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35010779	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35622181	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628210	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36036948	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089581	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41284358	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55711292	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60820172	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61867966	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61867967	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61868018	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585309	1.00[JPT][hapmap]
rs6585310	1.00[JPT][hapmap]
rs6585311	1.00[JPT][hapmap]
rs68085797	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071789	1.00[JPT][hapmap]
rs7071812	1.00[JPT][hapmap]
rs7072356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072364	1.00[ASN][1000 genomes]
rs7074729	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075888	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089973	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7093674	1.00[ASN][1000 genomes]
rs7094072	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099565	1.00[JPT][hapmap]
rs7099590	1.00[JPT][hapmap]
rs7100026	1.00[JPT][hapmap]
rs749649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895551	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898249	1.00[JPT][hapmap]
rs7904605	1.00[JPT][hapmap]
rs7908069	1.00[JPT][hapmap]
rs7908464	1.00[JPT][hapmap]
rs7909566	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909657	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918253	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918388	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923295	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881192	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17794346	FAM160B1	cis	Adipose Subcutaneous	GTEx
rs17794346	ALDH1A1	cis	Brain Pons	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116641600-116645400	Weak transcription	Stomach Mucosa	stomach
2	chr10:116642000-116643200	Enhancers	Colon Smooth Muscle	Colon
3	chr10:116642000-116643200	Enhancers	Hela-S3	cervix
4	chr10:116642200-116643200	Enhancers	HMEC	breast
5	chr10:116642200-116655800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr10:116642600-116643200	Enhancers	A549	lung

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