Variant report

Variant	rs4420169
Chromosome Location	chr10:28188681-28188682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr10:28188402-28188740	HepG2	liver:	n/a	n/a
2	SP1	chr10:28188338-28188789	HepG2	liver:	n/a	n/a
3	FOXA1	chr10:28188429-28188796	HepG2	liver:	n/a	n/a
4	FOXA1	chr10:28188373-28188818	HepG2	liver:	n/a	n/a
5	FOXA2	chr10:28188307-28188749	A549	lung:	n/a	n/a
6	FOXA1	chr10:28188363-28188865	HepG2	liver:	n/a	n/a
7	JUND	chr10:28188434-28188703	HepG2	liver:	n/a	n/a
8	FOXA2	chr10:28188447-28188716	HepG2	liver:	n/a	n/a
9	FOSL2	chr10:28188475-28188719	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RPL36AP55	TF binding region

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10826357	0.92[ASN][1000 genomes]
rs10826358	0.92[ASN][1000 genomes]
rs10826359	0.93[ASN][1000 genomes]
rs10826360	0.93[ASN][1000 genomes]
rs10826362	0.96[ASN][1000 genomes]
rs10826363	0.93[ASN][1000 genomes]
rs10826364	0.93[ASN][1000 genomes]
rs10826365	0.94[ASN][1000 genomes]
rs10826370	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11006758	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11006759	0.93[ASN][1000 genomes]
rs11006760	0.95[ASN][1000 genomes]
rs11006761	0.95[ASN][1000 genomes]
rs11006762	0.95[ASN][1000 genomes]
rs11006764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006765	0.96[ASN][1000 genomes]
rs11006766	0.96[ASN][1000 genomes]
rs11006767	0.96[ASN][1000 genomes]
rs11006769	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11006779	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11006786	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11492473	0.96[ASN][1000 genomes]
rs11595397	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11595783	0.93[ASN][1000 genomes]
rs11596317	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11598344	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11816757	0.93[ASN][1000 genomes]
rs12358199	0.93[ASN][1000 genomes]
rs12358283	0.93[ASN][1000 genomes]
rs12772278	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12779352	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1334719	0.93[ASN][1000 genomes]
rs1413772	0.95[ASN][1000 genomes]
rs1419366	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1832005	0.96[ASN][1000 genomes]
rs1931889	0.87[ASN][1000 genomes]
rs1970631	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2003192	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2065690	0.94[ASN][1000 genomes]
rs2184418	0.96[ASN][1000 genomes]
rs2297646	0.87[ASN][1000 genomes]
rs2368271	0.96[ASN][1000 genomes]
rs2368272	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2368273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2368274	0.93[ASN][1000 genomes]
rs3824590	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3952837	0.85[ASN][1000 genomes]
rs4237386	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4265508	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4303140	0.86[EUR][1000 genomes]
rs4494226	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4590766	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4600119	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4628591	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4749274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4749275	0.95[ASN][1000 genomes]
rs4749276	0.95[ASN][1000 genomes]
rs4749277	0.95[ASN][1000 genomes]
rs4749278	0.96[ASN][1000 genomes]
rs4749279	0.96[ASN][1000 genomes]
rs4749280	0.96[ASN][1000 genomes]
rs4749285	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4749286	0.82[EUR][1000 genomes]
rs4749287	0.84[EUR][1000 genomes]
rs6481490	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6481491	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7070860	0.95[ASN][1000 genomes]
rs7074562	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7077472	0.93[ASN][1000 genomes]
rs7087095	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7089040	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7090390	0.92[ASN][1000 genomes]
rs7094167	0.95[ASN][1000 genomes]
rs7094542	0.96[ASN][1000 genomes]
rs7095239	0.88[ASN][1000 genomes]
rs7095692	0.93[ASN][1000 genomes]
rs7099583	0.92[ASN][1000 genomes]
rs7099871	0.93[ASN][1000 genomes]
rs7099876	0.94[ASN][1000 genomes]
rs7100494	0.92[ASN][1000 genomes]
rs7893462	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7896951	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7897553	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7897889	0.93[ASN][1000 genomes]
rs7907415	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7907500	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7924172	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs880706	0.93[ASN][1000 genomes]
rs880707	0.93[ASN][1000 genomes]
rs880708	0.93[ASN][1000 genomes]
rs9663255	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831813	chr10:28017606-28200651	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28188000-28189000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:28188000-28189000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:28188000-28189000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:28188000-28189200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr10:28188000-28189200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr10:28188000-28189400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr10:28188000-28189600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:28188000-28189600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr10:28188000-28189600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr10:28188200-28189000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr10:28188200-28189000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr10:28188200-28189000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr10:28188200-28189000	Enhancers	Dnd41	blood
14	chr10:28188200-28189200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr10:28188200-28189200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:28188200-28189200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr10:28188200-28189200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr10:28188200-28189200	Enhancers	Fetal Thymus	thymus
19	chr10:28188200-28189200	Enhancers	Stomach Mucosa	stomach
20	chr10:28188200-28189400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr10:28188200-28189600	Enhancers	Primary T cells from cord blood	blood
22	chr10:28188400-28188800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr10:28188400-28188800	Active TSS	HepG2	liver
24	chr10:28188400-28189000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr10:28188400-28189000	Enhancers	Liver	Liver
26	chr10:28188400-28189200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr10:28188400-28190600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr10:28188400-28214000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:28188600-28189000	Active TSS	Duodenum Mucosa	Duodenum
30	chr10:28188600-28189200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr10:28188600-28189200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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