Variant report

Variant	rs11733473
Chromosome Location	chr4:152189368-152189369
allele	A/C
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	FOS	chr4:152189036-152189639	MCF10A-Er-Src	breast:	n/a	n/a
2	CREB1	chr4:152188904-152189449	HepG2	liver:	n/a	n/a
3	STAT3	chr4:152189113-152189490	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr4:152189087-152189642	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr4:152189073-152189376	A549	lung:	n/a	chr4:152189158-152189169
6	STAT3	chr4:152189131-152189610	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr4:152189077-152189589	MCF10A-Er-Src	breast:	n/a	chr4:152189079-152189087
8	FOS	chr4:152189083-152189642	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr4:152188968-152189381	HepG2	liver:	n/a	chr4:152189158-152189169

Variant related genes	Relation type
SH3D19	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10006091	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10011948	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10012999	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10015834	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs10016704	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10019075	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10031618	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10031902	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857257	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099797	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099798	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099799	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099801	0.94[EUR][1000 genomes]
rs11099802	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11721421	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11726496	0.84[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11729901	0.93[EUR][1000 genomes]
rs11730707	0.94[EUR][1000 genomes]
rs11733501	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733600	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11734518	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11734727	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11735681	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12501397	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12505382	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12508449	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17590780	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2291978	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407166	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28650996	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28651657	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28760401	0.82[EUR][1000 genomes]
rs28767036	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35245353	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3990708	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4339187	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4417949	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4473634	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55812154	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55855806	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55869644	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs55905531	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs56220030	0.97[EUR][1000 genomes]
rs62328350	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62328351	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62328353	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6535780	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6535781	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6535782	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6535783	0.83[EUR][1000 genomes]
rs6535785	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6823844	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824159	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824195	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6832149	0.83[EUR][1000 genomes]
rs6844983	0.92[EUR][1000 genomes]
rs6849871	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6849875	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6851493	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72725927	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7663659	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7665657	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7689875	0.82[EUR][1000 genomes]
rs7695360	0.93[EUR][1000 genomes]
rs9985620	0.82[AMR][1000 genomes]
rs9990564	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9994652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996742	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9997353	0.82[EUR][1000 genomes]
rs9997461	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152149200-152197600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:152172800-152190600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:152173400-152189400	Weak transcription	Aorta	Aorta
4	chr4:152173800-152198200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:152174000-152192200	Weak transcription	Brain Angular Gyrus	brain
6	chr4:152177400-152198200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:152177800-152200000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:152180000-152193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:152180800-152191000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:152182600-152211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:152182800-152206000	Weak transcription	NHEK	skin
12	chr4:152183200-152198200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:152184400-152192400	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:152185000-152191200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:152185000-152198200	Weak transcription	Right Ventricle	heart
16	chr4:152185200-152197600	Weak transcription	Left Ventricle	heart
17	chr4:152187000-152189400	Enhancers	HepG2	liver
18	chr4:152187400-152189400	Enhancers	Fetal Intestine Small	intestine
19	chr4:152187600-152189400	Enhancers	Fetal Intestine Large	intestine
20	chr4:152188600-152204000	Weak transcription	Gastric	stomach
21	chr4:152188800-152189400	Enhancers	Stomach Mucosa	stomach
22	chr4:152189000-152189400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:152189000-152189400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:152189000-152189400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr4:152189000-152189600	Genic enhancers	Duodenum Mucosa	Duodenum
26	chr4:152189200-152195400	Weak transcription	Psoas Muscle	Psoas
27	chr4:152189200-152197600	Weak transcription	Ovary	ovary

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