Variant report

Variant	rs11733501
Chromosome Location	chr4:152189524-152189525
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	FOS	chr4:152189036-152189639	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr4:152189087-152189642	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr4:152189131-152189610	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr4:152189077-152189589	MCF10A-Er-Src	breast:	n/a	chr4:152189079-152189087
5	FOS	chr4:152189083-152189642	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SH3D19	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10006091	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10011948	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10012999	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10015834	0.92[EUR][1000 genomes]
rs10016704	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10019075	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10031618	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10031902	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857257	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099797	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099798	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099799	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099801	0.99[EUR][1000 genomes]
rs11099802	0.94[EUR][1000 genomes]
rs11721421	0.93[EUR][1000 genomes]
rs11726496	0.94[EUR][1000 genomes]
rs11729901	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11730707	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11733473	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733600	0.94[EUR][1000 genomes]
rs11734518	0.94[EUR][1000 genomes]
rs11734727	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11735681	0.93[EUR][1000 genomes]
rs12501397	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12505382	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12508449	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17590780	0.94[EUR][1000 genomes]
rs2291978	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407166	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28650996	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28651657	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28767036	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35245353	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3990708	0.94[EUR][1000 genomes]
rs4339187	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4417949	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4473634	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55812154	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55855806	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55869644	0.94[EUR][1000 genomes]
rs55905531	0.94[EUR][1000 genomes]
rs56220030	0.92[EUR][1000 genomes]
rs62328350	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62328351	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62328353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6535780	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6535781	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6535782	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6535785	0.94[EUR][1000 genomes]
rs6823844	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824159	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824195	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6844983	0.97[EUR][1000 genomes]
rs6849871	0.94[EUR][1000 genomes]
rs6849875	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6851493	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72725927	0.94[EUR][1000 genomes]
rs7663659	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7665657	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7695360	0.98[EUR][1000 genomes]
rs9990564	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9994652	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996742	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9997461	0.87[AFR][1000 genomes];0.99[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	chr4:152173800-152198200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:152174000-152192200	Weak transcription	Brain Angular Gyrus	brain
5	chr4:152177400-152198200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:152177800-152200000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:152180000-152193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:152180800-152191000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:152182600-152211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:152182800-152206000	Weak transcription	NHEK	skin
11	chr4:152183200-152198200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:152184400-152192400	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:152185000-152191200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:152185000-152198200	Weak transcription	Right Ventricle	heart
15	chr4:152185200-152197600	Weak transcription	Left Ventricle	heart
16	chr4:152188600-152204000	Weak transcription	Gastric	stomach
17	chr4:152189000-152189600	Genic enhancers	Duodenum Mucosa	Duodenum
18	chr4:152189200-152195400	Weak transcription	Psoas Muscle	Psoas
19	chr4:152189200-152197600	Weak transcription	Ovary	ovary
20	chr4:152189400-152189600	Enhancers	Fetal Kidney	kidney
21	chr4:152189400-152193600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:152189400-152193800	Weak transcription	Stomach Mucosa	stomach
23	chr4:152189400-152197600	Weak transcription	Fetal Intestine Small	intestine
24	chr4:152189400-152197600	Weak transcription	HepG2	liver
25	chr4:152189400-152198200	Weak transcription	Fetal Intestine Large	intestine
26	chr4:152189400-152202400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:152189400-152205800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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