Variant report

Variant	rs16960644
Chromosome Location	chr17:19953617-19953618
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	chr17:19945642..19947610-chr17:19953431..19955992,2	MCF-7	breast:
2	chr17:19950835..19953752-chr17:19957285..19959162,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1034904	0.89[ASN][1000 genomes]
rs10459970	0.82[AMR][1000 genomes]
rs11867585	0.91[JPT][hapmap]
rs119672	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs12051550	0.89[GIH][hapmap];0.88[MEX][hapmap]
rs1479129	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs169412	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs16960717	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs16960730	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs16964352	0.89[GIH][hapmap];0.88[MEX][hapmap]
rs175922	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1860302	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1971043	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs1971044	1.00[CEU][hapmap]
rs203450	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs203457	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs203458	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs203460	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs203462	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs203465	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs203466	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs203477	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs203479	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs203481	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2042046	0.85[JPT][hapmap]
rs2108978	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2108979	0.89[ASN][1000 genomes]
rs2108980	0.84[ASN][1000 genomes]
rs2385960	0.82[AMR][1000 genomes]
rs28807825	0.89[ASN][1000 genomes]
rs35003563	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs3764436	0.89[GIH][hapmap];0.88[MEX][hapmap]
rs3909258	0.91[ASN][1000 genomes]
rs397969	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4924801	0.85[ASN][1000 genomes]
rs4924803	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4925060	0.85[JPT][hapmap]
rs4925065	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4925066	0.85[ASN][1000 genomes]
rs4925067	0.85[ASN][1000 genomes]
rs4925069	0.92[ASN][1000 genomes]
rs4925072	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4925077	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4925081	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs57040439	0.82[AMR][1000 genomes]
rs57673732	0.82[AMR][1000 genomes]
rs58313980	0.82[AMR][1000 genomes]
rs7207625	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7208025	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7208365	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7209734	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7211535	0.86[ASN][1000 genomes]
rs7213816	1.00[CEU][hapmap]
rs7215097	0.93[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs7222403	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs73984559	0.82[AMR][1000 genomes]
rs8065337	0.89[ASN][1000 genomes]
rs8073875	0.82[AMR][1000 genomes]
rs850623	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs860335	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs888423	0.87[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap]
rs918227	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9891739	0.91[ASN][1000 genomes]
rs9911605	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap]
rs9941362	1.00[CEU][hapmap]
rs9941376	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1066594	chr17:19947874-19986671	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv543259	chr17:19947874-19986671	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16960644	AKAP10	cis	Whole Blood	GTEx
rs16960644	AKAP10	cis	multi-tissue	Pritchard
rs16960644	AKAP10	cis	lymphoblastoid	seeQTL
rs16960644	ALDH3A1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19923400-19956600	Weak transcription	A549	lung
2	chr17:19932000-19956800	Weak transcription	Ovary	ovary
3	chr17:19943800-19965800	Weak transcription	Aorta	Aorta
4	chr17:19945800-19956000	Weak transcription	K562	blood
5	chr17:19948200-19966400	Weak transcription	Brain Angular Gyrus	brain
6	chr17:19950800-19966400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr17:19951200-19956800	Weak transcription	Left Ventricle	heart

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