Variant report

Variant	rs11099790
Chromosome Location	chr4:152111770-152111771
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	chr4:152111558..152113279-chr4:152114907..152117162,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10000557	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10001039	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10005907	0.85[ASN][1000 genomes]
rs10016998	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10030785	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10032477	0.80[ASN][1000 genomes]
rs10213332	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1046168	0.80[ASN][1000 genomes]
rs10776521	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10776523	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10857254	0.82[ASN][1000 genomes]
rs10857255	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10964	0.80[ASN][1000 genomes]
rs11099783	0.80[ASN][1000 genomes]
rs11099787	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11099788	0.87[ASN][1000 genomes]
rs11099791	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11099794	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11099795	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11723219	0.80[ASN][1000 genomes]
rs11726180	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11729981	0.80[ASN][1000 genomes]
rs11730087	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11734586	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11938266	0.80[ASN][1000 genomes]
rs11943477	0.84[EUR][1000 genomes]
rs12500168	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12500223	0.80[ASN][1000 genomes]
rs12507657	0.80[ASN][1000 genomes]
rs13123932	0.85[ASN][1000 genomes]
rs13149045	0.80[ASN][1000 genomes]
rs1316364	0.80[ASN][1000 genomes]
rs1320006	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1320007	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1320192	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1878796	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2407406	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2407411	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2407414	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2407415	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2407424	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2407425	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2407426	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2407427	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2407428	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2407429	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2407430	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2407439	0.80[ASN][1000 genomes]
rs2407440	0.82[ASN][1000 genomes]
rs2897657	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2897660	0.82[ASN][1000 genomes]
rs4434229	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4616734	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4696235	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4696237	0.80[ASN][1000 genomes]
rs6535766	0.80[ASN][1000 genomes]
rs6535767	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6535776	0.80[ASN][1000 genomes]
rs6812695	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6823953	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6825613	0.82[ASN][1000 genomes]
rs6825952	0.82[ASN][1000 genomes]
rs6828937	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6829963	0.82[ASN][1000 genomes]
rs6837905	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6838301	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6838845	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6847669	0.80[ASN][1000 genomes]
rs6853215	0.80[ASN][1000 genomes]
rs6856569	0.84[EUR][1000 genomes]
rs7659146	0.80[ASN][1000 genomes]
rs7666751	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7668154	0.82[ASN][1000 genomes]
rs7681030	0.80[ASN][1000 genomes]
rs7683092	0.80[ASN][1000 genomes]
rs7687117	0.80[ASN][1000 genomes]
rs7689095	0.80[ASN][1000 genomes]
rs7690329	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7695005	0.80[ASN][1000 genomes]
rs938990	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152088200-152114600	Weak transcription	Psoas Muscle	Psoas
2	chr4:152096600-152118000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:152096800-152120600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:152097200-152123600	Weak transcription	Pancreas	Pancrea
5	chr4:152097200-152136600	Weak transcription	Colonic Mucosa	Colon
6	chr4:152097400-152123600	Weak transcription	Aorta	Aorta
7	chr4:152097600-152128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:152097800-152117200	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:152097800-152120000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:152098200-152117000	Weak transcription	Brain Anterior Caudate	brain
11	chr4:152098200-152118400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:152098400-152116600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:152098400-152118400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:152098400-152147200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:152100200-152116600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:152100600-152118000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr4:152106400-152112200	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:152106600-152112200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:152106600-152115600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:152106600-152116600	Weak transcription	NHEK	skin
21	chr4:152106600-152117200	Weak transcription	Left Ventricle	heart
22	chr4:152106800-152111800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:152106800-152111800	Weak transcription	Fetal Intestine Large	intestine
24	chr4:152106800-152113800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:152106800-152116600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:152107200-152116000	Weak transcription	Ovary	ovary
27	chr4:152107200-152120000	Weak transcription	HepG2	liver
28	chr4:152107600-152113400	Weak transcription	Fetal Heart	heart
29	chr4:152107600-152116600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:152110000-152113600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:152110200-152113800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:152110800-152111800	Enhancers	Adipose Nuclei	Adipose
33	chr4:152110800-152112600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
34	chr4:152110800-152113400	ZNF genes & repeats	Fetal Intestine Small	intestine
35	chr4:152111400-152111800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:152111400-152112200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:152111400-152112400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
38	chr4:152111400-152112400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:152111400-152112800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:152111600-152111800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
41	chr4:152111600-152112000	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr4:152111600-152112000	ZNF genes & repeats	Lung	lung
43	chr4:152111600-152112200	ZNF genes & repeats	Fetal Stomach	stomach
44	chr4:152111600-152112200	Enhancers	Right Atrium	heart
45	chr4:152111600-152112200	Enhancers	Right Ventricle	heart
46	chr4:152111600-152112400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:152111600-152112600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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