Variant report

Variant	rs17802416
Chromosome Location	chr8:104368673-104368674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:104310756..104313273-chr8:104365945..104369337,3	MCF-7	breast:
2	chr8:104367544..104369608-chr8:104383026..104384896,2	MCF-7	breast:
3	chr8:104363177..104365270-chr8:104368358..104371064,2	MCF-7	breast:
4	chr8:104367758..104370147-chr8:104374121..104376072,2	MCF-7	breast:
5	chr8:104365094..104368478-chr8:104368534..104371541,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247081	Chromatin interaction
ENSG00000164932	Chromatin interaction
ENSG00000164930	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10089343	1.00[CHB][hapmap]
rs10090069	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10093100	0.82[AMR][1000 genomes]
rs10093198	0.82[AMR][1000 genomes]
rs10094939	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10096207	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10097121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10100283	0.82[AMR][1000 genomes]
rs10101517	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10102413	1.00[CHB][hapmap]
rs10105195	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10105450	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10108112	0.83[EUR][1000 genomes]
rs10109642	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10112317	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10112450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10112941	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10112952	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10113160	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10113367	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1032471	1.00[CHB][hapmap]
rs1061196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11781628	1.00[CHB][hapmap]
rs11785583	1.00[CHB][hapmap]
rs11985002	0.98[EUR][1000 genomes]
rs13255562	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13257958	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13263611	1.00[CHB][hapmap]
rs13266347	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13266642	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13278335	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13282967	1.00[CHB][hapmap]
rs1370007	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17205821	1.00[CHB][hapmap]
rs17228538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17802518	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17804088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17804149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs28437723	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28862349	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2948449	1.00[CHB][hapmap]
rs3104026	1.00[CHB][hapmap]
rs35225263	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35392014	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57237927	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6985718	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6989714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6990501	1.00[CHB][hapmap]
rs71520811	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72675443	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72675444	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72675445	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7818129	0.82[AMR][1000 genomes]
rs7820626	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7839421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7845210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs827528	1.00[CHB][hapmap]
rs827537	1.00[CHB][hapmap]
rs827546	1.00[CHB][hapmap]
rs951826	1.00[CHB][hapmap]
rs973242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs981816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1020476	chr8:104312212-104924482	Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv539704	chr8:104312212-104924482	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1016395	chr8:104327541-104473005	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1023048	chr8:104355188-104872701	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv539705	chr8:104355188-104872701	ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1021345	chr8:104361854-104879684	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1032085	chr8:104362187-104878345	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv397277	chr8:104368395-104374284	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17802416	ANKRD46	cis	parietal	SCAN
rs17802416	SLC25A32	cis	parietal	SCAN
rs17802416	FZD6	Cis_1M	lymphoblastoid	RTeQTL
rs17802416	DCAF13	cis	cerebellum	SCAN
rs17802416	FZD6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104357800-104383400	Weak transcription	Aorta	Aorta
2	chr8:104363000-104369200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr8:104363000-104371800	Weak transcription	HSMMtube	muscle
4	chr8:104363200-104372200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:104363600-104369000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:104364000-104369200	Weak transcription	Fetal Stomach	stomach
7	chr8:104364200-104368800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr8:104365600-104369400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr8:104366800-104369200	Weak transcription	Thymus	Thymus
10	chr8:104366800-104372000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr8:104366800-104372000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:104367000-104368800	Weak transcription	Fetal Thymus	thymus
13	chr8:104367000-104371800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr8:104367200-104372400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr8:104368600-104369400	Enhancers	Brain Hippocampus Middle	brain

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