Variant report

Variant	rs854804
Chromosome Location	chr17:18067404-18067405
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	chr17:18065336..18068022-chr17:18085944..18088320,2	MCF-7	breast:
2	chr17:18063606..18070028-chr17:18081885..18087934,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091542	Chromatin interaction
ENSG00000266677	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11869205	0.90[ASN][1000 genomes]
rs11870766	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11871970	0.90[ASN][1000 genomes]
rs12150618	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12451754	0.83[ASN][1000 genomes]
rs12936694	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12937300	0.90[CHD][hapmap]
rs12939469	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12939757	0.90[CHD][hapmap]
rs12945597	0.90[CHD][hapmap]
rs12946842	0.87[ASN][1000 genomes]
rs12952556	0.90[CHD][hapmap]
rs1378601	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1378602	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563631	0.90[CHD][hapmap]
rs1979276	0.90[CHD][hapmap]
rs2245737	0.88[GIH][hapmap]
rs2273028	0.90[CHD][hapmap]
rs2360234	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2461838	0.90[CHD][hapmap]
rs2605135	0.95[GIH][hapmap];0.84[TSI][hapmap]
rs2605136	0.81[CHD][hapmap]
rs2605142	0.90[CHD][hapmap]
rs2746025	0.90[CHD][hapmap]
rs2746027	0.90[CHD][hapmap]
rs2746028	0.88[GIH][hapmap];0.84[TSI][hapmap]
rs2746029	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs28641923	0.85[ASN][1000 genomes]
rs2925137	0.90[ASN][1000 genomes]
rs2925138	0.90[ASN][1000 genomes]
rs3794782	0.83[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4603612	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs4924839	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924840	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4924841	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4925149	0.81[ASN][1000 genomes]
rs4925150	0.81[ASN][1000 genomes]
rs4925171	0.90[CHD][hapmap]
rs56021431	0.90[ASN][1000 genomes]
rs643333	0.90[CHD][hapmap]
rs712270	0.86[JPT][hapmap]
rs712273	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712275	0.85[ASN][1000 genomes]
rs7207123	0.81[CHD][hapmap]
rs7207306	0.90[CHD][hapmap]
rs7212808	0.86[ASN][1000 genomes]
rs7215839	0.90[CHD][hapmap]
rs8069321	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8071834	1.00[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs854771	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs854772	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs854775	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854776	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs854779	0.88[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs854781	0.83[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs854795	0.93[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs854797	0.87[ASN][1000 genomes]
rs854798	0.92[ASN][1000 genomes]
rs854799	0.87[ASN][1000 genomes]
rs854801	0.90[ASN][1000 genomes]
rs854805	0.92[ASN][1000 genomes]
rs854806	0.92[ASN][1000 genomes]
rs854807	0.92[ASN][1000 genomes]
rs860567	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs860568	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs865923	0.92[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs921986	0.90[CHD][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	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs854804	FLII	cis	cerebellum	SCAN
rs854804	TOP3A	cis	cerebellum	SCAN
rs854804	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs854804	MYO15A	cis	cerebellum	SCAN
rs854804	LRRC48	cis	parietal	SCAN
rs854804	LGALS9C	cis	Whole Blood	GTEx
rs854804	LOC162632	cis	parietal	SCAN
rs854804	AKAP10	cis	cerebellum	SCAN
rs854804	LOC162632	cis	cerebellum	SCAN
rs854804	SHMT1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18062000-18085600	Weak transcription	Brain Angular Gyrus	brain
2	chr17:18062200-18067600	Enhancers	K562	blood
3	chr17:18062200-18085000	Weak transcription	Right Atrium	heart
4	chr17:18062600-18070000	Weak transcription	Ovary	ovary
5	chr17:18064800-18085400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr17:18065400-18067800	Enhancers	Spleen	Spleen
7	chr17:18065600-18069600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr17:18066000-18069600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:18066400-18067800	Enhancers	Fetal Intestine Large	intestine
10	chr17:18066400-18067800	Enhancers	Fetal Intestine Small	intestine
11	chr17:18067000-18070400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:18067400-18069800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr17:18067400-18070600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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