Variant report

Variant	rs7687117
Chromosome Location	chr4:152153617-152153618
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	E2F4	chr4:152153540-152153683	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:152153555-152153653	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SH3D19	TF binding region

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10000557	0.93[ASN][1000 genomes]
rs10001039	0.93[ASN][1000 genomes]
rs10005907	0.90[ASN][1000 genomes]
rs10011421	0.83[ASN][1000 genomes]
rs10016092	0.80[EUR][1000 genomes]
rs10016998	1.00[ASN][1000 genomes]
rs10017154	0.85[ASN][1000 genomes]
rs10020297	0.80[EUR][1000 genomes]
rs10030785	0.90[ASN][1000 genomes]
rs10032477	0.85[ASN][1000 genomes]
rs10213332	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1046168	0.85[ASN][1000 genomes]
rs10776521	0.93[ASN][1000 genomes]
rs10776523	0.93[ASN][1000 genomes]
rs10857254	0.88[ASN][1000 genomes]
rs10857255	0.93[ASN][1000 genomes]
rs10857256	0.90[ASN][1000 genomes]
rs10964	0.85[ASN][1000 genomes]
rs11099783	0.85[ASN][1000 genomes]
rs11099787	0.88[ASN][1000 genomes]
rs11099788	0.93[ASN][1000 genomes]
rs11099790	0.80[ASN][1000 genomes]
rs11099791	0.93[ASN][1000 genomes]
rs11099794	1.00[ASN][1000 genomes]
rs11099795	1.00[ASN][1000 genomes]
rs11723219	0.85[ASN][1000 genomes]
rs11726180	0.93[ASN][1000 genomes]
rs11729981	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730087	1.00[ASN][1000 genomes]
rs11734586	0.93[ASN][1000 genomes]
rs11938266	0.85[ASN][1000 genomes]
rs11943477	0.97[ASN][1000 genomes]
rs12500168	0.93[ASN][1000 genomes]
rs12500223	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507657	0.85[ASN][1000 genomes]
rs13103344	0.80[EUR][1000 genomes]
rs13123932	0.90[ASN][1000 genomes]
rs13148755	0.81[ASN][1000 genomes]
rs13149045	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1316364	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320006	1.00[ASN][1000 genomes]
rs1320007	1.00[ASN][1000 genomes]
rs1320192	1.00[ASN][1000 genomes]
rs1878796	1.00[ASN][1000 genomes]
rs2407223	0.80[EUR][1000 genomes]
rs2407406	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2407411	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2407414	1.00[ASN][1000 genomes]
rs2407415	1.00[ASN][1000 genomes]
rs2407424	0.93[ASN][1000 genomes]
rs2407425	0.93[ASN][1000 genomes]
rs2407426	0.93[ASN][1000 genomes]
rs2407427	0.88[ASN][1000 genomes]
rs2407428	0.93[ASN][1000 genomes]
rs2407429	0.93[ASN][1000 genomes]
rs2407430	0.88[ASN][1000 genomes]
rs2407439	0.85[ASN][1000 genomes]
rs2407440	0.88[ASN][1000 genomes]
rs2407441	0.81[ASN][1000 genomes]
rs2897657	1.00[ASN][1000 genomes]
rs2897660	0.88[ASN][1000 genomes]
rs4434229	0.93[ASN][1000 genomes]
rs4467540	0.80[EUR][1000 genomes]
rs4591577	0.80[EUR][1000 genomes]
rs4616734	1.00[ASN][1000 genomes]
rs4640649	0.83[ASN][1000 genomes]
rs4696229	0.83[ASN][1000 genomes]
rs4696235	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4696237	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535766	0.85[ASN][1000 genomes]
rs6535767	0.88[ASN][1000 genomes]
rs6535775	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6535776	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535777	0.81[ASN][1000 genomes]
rs6812695	0.93[ASN][1000 genomes]
rs6815608	0.93[ASN][1000 genomes]
rs6823953	1.00[ASN][1000 genomes]
rs6825613	0.88[ASN][1000 genomes]
rs6825952	0.88[ASN][1000 genomes]
rs6828937	1.00[ASN][1000 genomes]
rs6829963	0.88[ASN][1000 genomes]
rs6837905	0.93[ASN][1000 genomes]
rs6838301	1.00[ASN][1000 genomes]
rs6838845	1.00[ASN][1000 genomes]
rs6847669	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853215	0.85[ASN][1000 genomes]
rs6856569	0.93[ASN][1000 genomes]
rs7659146	0.85[ASN][1000 genomes]
rs7666751	1.00[ASN][1000 genomes]
rs7668154	0.88[ASN][1000 genomes]
rs7681030	1.00[ASN][1000 genomes]
rs7683092	0.85[ASN][1000 genomes]
rs7689095	0.85[ASN][1000 genomes]
rs7690329	1.00[ASN][1000 genomes]
rs7695005	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938990	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv870229	chr4:152114410-152161072	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152120800-152153800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:152129000-152168000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:152129400-152167800	Weak transcription	Right Ventricle	heart
4	chr4:152130200-152187800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:152136600-152158000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:152141000-152167400	Weak transcription	HepG2	liver
7	chr4:152144800-152163400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:152147200-152160200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:152148000-152158000	Weak transcription	Fetal Intestine Small	intestine
10	chr4:152148000-152164200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:152148200-152158200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:152148200-152163400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:152149200-152155000	Weak transcription	Brain Anterior Caudate	brain
14	chr4:152149200-152156200	Weak transcription	Pancreas	Pancrea
15	chr4:152149200-152157200	Weak transcription	Fetal Intestine Large	intestine
16	chr4:152149200-152159200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:152149200-152172000	Weak transcription	Left Ventricle	heart
18	chr4:152149200-152185200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:152149200-152197600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr4:152149600-152154800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:152149600-152158200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:152149600-152159600	Weak transcription	Brain Angular Gyrus	brain
23	chr4:152149600-152173000	Weak transcription	Right Atrium	heart
24	chr4:152149800-152154800	Weak transcription	Brain Substantia Nigra	brain
25	chr4:152150200-152153800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:152150200-152155600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:152150200-152157000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:152150200-152158600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:152150400-152154000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:152151000-152156800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:152151000-152157200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:152151200-152154800	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:152151400-152158200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:152151600-152154800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:152152400-152159800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:152152800-152153800	Enhancers	Fetal Lung	lung
37	chr4:152152800-152153800	Enhancers	Fetal Stomach	stomach
38	chr4:152152800-152154000	Enhancers	Adipose Nuclei	Adipose
39	chr4:152152800-152154200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:152152800-152154200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr4:152153000-152153800	Enhancers	Placenta	Placenta
42	chr4:152153200-152154000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:152153200-152155000	Enhancers	Ovary	ovary
44	chr4:152153400-152154000	Weak transcription	Lung	lung
45	chr4:152153400-152154000	Weak transcription	Psoas Muscle	Psoas
46	chr4:152153400-152154000	Enhancers	HSMMtube	muscle
47	chr4:152153400-152154200	Enhancers	Colon Smooth Muscle	Colon
48	chr4:152153400-152154200	Enhancers	Fetal Heart	heart

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