Variant report

Variant	rs10005907
Chromosome Location	chr4:152113873-152113874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152108334..152110110-chr4:152112946..152114914,2	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10000557	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10001039	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10011421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10016998	0.90[ASN][1000 genomes]
rs10021054	0.88[EUR][1000 genomes]
rs10030785	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10032477	0.90[ASN][1000 genomes]
rs10213332	0.90[ASN][1000 genomes]
rs10222881	1.00[JPT][hapmap]
rs1046168	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10776521	0.97[ASN][1000 genomes]
rs10776523	0.97[ASN][1000 genomes]
rs10857254	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10857255	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10857256	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10964	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11099782	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11099783	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11099787	0.93[ASN][1000 genomes]
rs11099788	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11099790	0.85[ASN][1000 genomes]
rs11099791	0.97[ASN][1000 genomes]
rs11099794	0.90[ASN][1000 genomes]
rs11099795	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11723219	0.90[ASN][1000 genomes]
rs11726180	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11729981	0.90[ASN][1000 genomes]
rs11730087	0.90[ASN][1000 genomes]
rs11734586	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11938266	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11943477	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12500168	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12500223	0.90[ASN][1000 genomes]
rs12507657	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13123932	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125574	1.00[JPT][hapmap]
rs13146584	1.00[JPT][hapmap]
rs13149045	0.90[ASN][1000 genomes]
rs1316364	0.90[ASN][1000 genomes]
rs1320006	0.90[ASN][1000 genomes]
rs1320007	0.90[ASN][1000 genomes]
rs1320192	0.90[ASN][1000 genomes]
rs1878796	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2407406	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2407411	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2407414	0.90[ASN][1000 genomes]
rs2407415	0.90[ASN][1000 genomes]
rs2407424	0.97[ASN][1000 genomes]
rs2407425	0.97[ASN][1000 genomes]
rs2407426	0.97[ASN][1000 genomes]
rs2407427	0.93[ASN][1000 genomes]
rs2407428	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2407429	0.97[ASN][1000 genomes]
rs2407430	0.93[ASN][1000 genomes]
rs2407439	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2407440	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2407441	0.86[ASN][1000 genomes]
rs2897657	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2897660	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4434229	0.97[ASN][1000 genomes]
rs4616734	0.90[ASN][1000 genomes]
rs4640649	0.88[ASN][1000 genomes]
rs4696226	1.00[JPT][hapmap]
rs4696229	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4696235	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4696237	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4696648	1.00[JPT][hapmap]
rs6535763	1.00[JPT][hapmap]
rs6535765	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6535766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6535767	0.93[ASN][1000 genomes]
rs6535775	0.86[ASN][1000 genomes]
rs6535776	0.90[ASN][1000 genomes]
rs6812695	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6815608	0.83[ASN][1000 genomes]
rs6819599	1.00[JPT][hapmap]
rs6823953	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6825613	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6825952	0.93[ASN][1000 genomes]
rs6826863	1.00[JPT][hapmap]
rs6828937	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6829963	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6833956	1.00[JPT][hapmap]
rs6837905	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6838301	0.90[ASN][1000 genomes]
rs6838845	0.90[ASN][1000 genomes]
rs6847669	0.90[ASN][1000 genomes]
rs6853215	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6856569	0.83[ASN][1000 genomes]
rs7659146	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7666751	0.90[ASN][1000 genomes]
rs7668154	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7678748	1.00[JPT][hapmap]
rs7681030	0.90[ASN][1000 genomes]
rs7683092	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7687117	0.90[ASN][1000 genomes]
rs7689095	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7690329	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7695005	0.90[ASN][1000 genomes]
rs7696634	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs938990	0.90[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:42 , 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	chr4:152106600-152115600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr4:152106600-152116600	Weak transcription	NHEK	skin
19	chr4:152106600-152117200	Weak transcription	Left Ventricle	heart
20	chr4:152106800-152116600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:152107200-152116000	Weak transcription	Ovary	ovary
22	chr4:152107200-152120000	Weak transcription	HepG2	liver
23	chr4:152107600-152116600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:152111800-152116600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:152112000-152117200	Weak transcription	Lung	lung
26	chr4:152112200-152116600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:152112200-152117200	Weak transcription	Right Atrium	heart
28	chr4:152112200-152120000	Weak transcription	Right Ventricle	heart
29	chr4:152112400-152117200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:152112400-152117200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:152112400-152120600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:152112600-152116000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:152112600-152117200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:152112600-152117400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:152112800-152120000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:152113400-152115000	Enhancers	Fetal Heart	heart
37	chr4:152113400-152124400	Weak transcription	Fetal Intestine Small	intestine
38	chr4:152113600-152114800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:152113600-152117200	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:152113800-152114800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:152113800-152114800	Enhancers	Adipose Nuclei	Adipose
42	chr4:152113800-152115800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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