Variant report

Variant	rs7897553
Chromosome Location	chr10:28201966-28201967
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	chr10:28198019..28200299-chr10:28200413..28203306,2	K562	blood:
2	chr10:28194965..28197519-chr10:28200097..28202641,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10826357	0.90[ASN][1000 genomes]
rs10826358	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs10826359	0.91[ASN][1000 genomes]
rs10826360	0.91[ASN][1000 genomes]
rs10826362	0.94[ASN][1000 genomes]
rs10826363	0.97[ASN][1000 genomes]
rs10826364	0.97[ASN][1000 genomes]
rs10826365	0.95[ASN][1000 genomes]
rs10826370	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11006758	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11006759	0.91[ASN][1000 genomes]
rs11006760	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs11006761	0.92[ASN][1000 genomes]
rs11006762	0.92[ASN][1000 genomes]
rs11006764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006765	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11006766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11006767	0.94[ASN][1000 genomes]
rs11006769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11006779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11006786	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11492473	0.94[ASN][1000 genomes]
rs11595397	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11595783	0.91[ASN][1000 genomes]
rs11596317	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11598344	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11816757	0.91[ASN][1000 genomes]
rs12355681	0.82[CEU][hapmap]
rs12358199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12358283	0.90[ASN][1000 genomes]
rs12772278	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12779352	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12780829	0.81[CEU][hapmap]
rs1334719	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1413772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1419366	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1832005	0.94[ASN][1000 genomes]
rs1931889	0.95[ASN][1000 genomes]
rs1970631	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2003192	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2065690	0.92[ASN][1000 genomes]
rs2184418	0.94[ASN][1000 genomes]
rs2297646	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2368271	0.94[ASN][1000 genomes]
rs2368272	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2368273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2368274	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3824590	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3952837	0.93[ASN][1000 genomes]
rs4237386	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4265508	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4303140	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4420169	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4494226	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4590766	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4600119	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4628591	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4749273	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4749274	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4749275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4749276	0.92[ASN][1000 genomes]
rs4749277	0.92[ASN][1000 genomes]
rs4749278	0.94[ASN][1000 genomes]
rs4749279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4749280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4749285	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4749286	0.84[EUR][1000 genomes]
rs4749287	0.96[CEU][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs6481490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6481491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7070860	0.92[ASN][1000 genomes]
rs7074562	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7077472	0.97[ASN][1000 genomes]
rs7087095	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7089040	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7090390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7094167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7094542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7095239	0.91[ASN][1000 genomes]
rs7095692	0.97[ASN][1000 genomes]
rs7099583	0.90[ASN][1000 genomes]
rs7099871	0.91[ASN][1000 genomes]
rs7099876	0.92[ASN][1000 genomes]
rs7100494	0.90[ASN][1000 genomes]
rs7893462	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7896951	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7897889	0.97[ASN][1000 genomes]
rs7907415	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7907500	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7924172	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs880706	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs880707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs880708	0.97[ASN][1000 genomes]
rs9663255	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv971859	chr10:28070066-28271252	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv894987	chr10:28165502-28326775	ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7897553	ZNF79	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28188400-28214000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:28195800-28203800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr10:28199800-28202000	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr10:28200800-28202400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr10:28201000-28202600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:28201200-28202000	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr10:28201200-28202200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr10:28201200-28202600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr10:28201400-28202400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr10:28201800-28204600	Weak transcription	Fetal Lung	lung

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