Variant report

Variant	rs13338946
Chromosome Location	chr16:30700858-30700859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30669894..30673951-chr16:30698340..30701082,5	MCF-7	breast:
2	chr16:30697796..30701437-chr16:30709412..30712126,4	MCF-7	breast:
3	chr16:30665347..30684079-chr16:30697204..30714344,66	MCF-7	breast:
4	chr16:30661852..30664336-chr16:30698718..30701457,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261840	Chromatin interaction
ENSG00000080603	Chromatin interaction
ENSG00000156858	Chromatin interaction
ENSG00000156860	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11150596	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs11864054	0.88[CHD][hapmap]
rs12918327	0.94[CHD][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs12926237	0.86[JPT][hapmap]
rs2289442	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35629860	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35969813	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747481	0.94[ASW][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3747486	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs3812999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs4616297	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889490	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4889614	0.93[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs4889630	0.86[JPT][hapmap]
rs4889651	0.81[GIH][hapmap]
rs4889653	0.81[GIH][hapmap]
rs6565201	0.85[EUR][1000 genomes]
rs67128646	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67456513	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186852	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs7187359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197475	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs7197770	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7204278	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7500719	0.88[ASW][hapmap];0.94[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap]
rs8046001	0.88[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs8046391	0.94[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap]
rs8048448	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8051050	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8055315	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8055661	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8058578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8058928	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8058961	0.94[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap]
rs885107	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9925025	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs9928572	0.81[EUR][1000 genomes]
rs9932572	0.86[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	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv469724	chr16:30632445-30840263	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv482704	chr16:30632445-30840263	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS 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	143 gene(s)	inside rSNPs	diseases
5	nsv833188	chr16:30632446-30840263	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
6	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
7	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
8	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
9	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
10	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13338946	C16orf93	cis	parietal	SCAN
rs13338946	RNF40	cis	cerebellum	SCAN
rs13338946	MYST1	cis	parietal	SCAN
rs13338946	MYST1	cis	cerebellum	SCAN
rs13338946	ZNF768	cis	parietal	SCAN
rs13338946	ITGAX	cis	parietal	SCAN
rs13338946	PHKG2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30682600-30705200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:30690000-30703000	Weak transcription	Fetal Intestine Small	intestine
3	chr16:30698800-30702200	Enhancers	Placenta	Placenta
4	chr16:30699800-30705000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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