Variant report

Variant	rs9933680
Chromosome Location	chr16:71548907-71548908
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71547709..71549497-chr16:71558790..71560524,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140835	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10500558	0.98[ASN][1000 genomes]
rs11640165	0.98[ASN][1000 genomes]
rs11641492	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11643101	0.86[CEU][hapmap]
rs11643216	0.98[ASN][1000 genomes]
rs11644434	0.81[CHB][hapmap]
rs11647749	0.98[ASN][1000 genomes]
rs12446461	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs13331346	0.91[ASN][1000 genomes]
rs1609868	0.88[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs1609869	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs16973266	0.82[CHB][hapmap]
rs172649	0.81[CHD][hapmap]
rs2004672	0.96[ASN][1000 genomes]
rs2070832	0.88[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2288486	0.94[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2288487	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs2288488	0.93[ASN][1000 genomes]
rs2303788	0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs2432524	0.88[CHB][hapmap]
rs28372238	0.96[ASN][1000 genomes]
rs310334	0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs35373081	0.90[ASN][1000 genomes]
rs35916432	0.91[ASN][1000 genomes]
rs3813743	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs4149498	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4503795	0.93[ASN][1000 genomes]
rs58134724	0.91[ASN][1000 genomes]
rs58452291	0.86[ASN][1000 genomes]
rs58719913	0.98[ASN][1000 genomes]
rs59819114	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6499523	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7184543	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7186241	0.98[ASN][1000 genomes]
rs7187165	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs7187354	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs7188342	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs7199026	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7199373	0.91[ASN][1000 genomes]
rs7200335	0.94[ASN][1000 genomes]
rs7200431	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs7202662	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs7202953	0.93[ASN][1000 genomes]
rs730470	0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs732318	0.88[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs74026831	0.98[ASN][1000 genomes]
rs74027246	0.98[ASN][1000 genomes]
rs8044068	0.96[ASN][1000 genomes]
rs8044561	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs8051212	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs8053662	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8058294	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs8058776	0.86[ASN][1000 genomes]
rs8061078	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs9302623	0.93[ASN][1000 genomes]
rs9926110	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs9928243	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9935426	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs9936249	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs9940771	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv906892	chr16:71526720-71570413	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9933680	HYDIN	cis	parietal	SCAN
rs9933680	COG8	cis	parietal	SCAN
rs9933680	CBFB	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71543400-71549800	Weak transcription	Pancreas	Pancrea
2	chr16:71547800-71549000	Enhancers	Colonic Mucosa	Colon
3	chr16:71548000-71549000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr16:71548600-71549200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr16:71548600-71549200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr16:71548600-71549400	Enhancers	Liver	Liver
7	chr16:71548800-71549200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr16:71548800-71549200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr16:71548800-71549400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr16:71548800-71549400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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