Variant report

Variant	rs13125574
Chromosome Location	chr4:152115283-152115284
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:
2	chr4:152114893..152116917-chr4:152120832..152122649,2	K562	blood:

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10000557	1.00[JPT][hapmap]
rs10001039	1.00[JPT][hapmap]
rs10005907	1.00[JPT][hapmap]
rs10011421	1.00[JPT][hapmap]
rs10016092	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10020297	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10020317	0.92[ASN][1000 genomes]
rs10030785	1.00[JPT][hapmap]
rs10222881	1.00[JPT][hapmap]
rs10434137	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10461254	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10461255	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1046168	1.00[JPT][hapmap]
rs10520101	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10520102	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10776522	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857254	1.00[JPT][hapmap]
rs10857255	1.00[JPT][hapmap]
rs10964	1.00[JPT][hapmap]
rs11099782	1.00[JPT][hapmap]
rs11099783	1.00[JPT][hapmap]
rs11099788	1.00[JPT][hapmap]
rs11099792	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11099793	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11099795	1.00[JPT][hapmap]
rs11099796	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11726180	1.00[JPT][hapmap]
rs11734577	0.93[ASN][1000 genomes]
rs11734586	1.00[JPT][hapmap]
rs11934792	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11938266	1.00[JPT][hapmap]
rs11943477	1.00[JPT][hapmap]
rs11945206	0.83[ASN][1000 genomes]
rs12500168	1.00[JPT][hapmap]
rs12505974	0.82[ASN][1000 genomes]
rs12507657	1.00[JPT][hapmap]
rs12644496	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12647306	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12648512	0.92[ASN][1000 genomes]
rs13103344	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13111753	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13122245	0.83[ASN][1000 genomes]
rs13122609	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13123932	1.00[JPT][hapmap]
rs13130167	0.83[ASN][1000 genomes]
rs13146584	1.00[JPT][hapmap]
rs1878796	1.00[JPT][hapmap]
rs2280280	0.82[ASN][1000 genomes]
rs2407222	0.83[ASN][1000 genomes]
rs2407223	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2407406	1.00[JPT][hapmap]
rs2407407	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407408	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407409	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407410	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407411	1.00[JPT][hapmap]
rs2407412	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407413	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2407417	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407418	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2407428	1.00[JPT][hapmap]
rs2407431	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407438	0.93[ASN][1000 genomes]
rs2407440	1.00[JPT][hapmap]
rs2897655	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2897656	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2897657	1.00[JPT][hapmap]
rs2897660	1.00[JPT][hapmap]
rs3792611	0.86[ASN][1000 genomes]
rs4266274	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4312738	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4467540	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4591577	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4696226	1.00[JPT][hapmap]
rs4696229	1.00[JPT][hapmap]
rs4696234	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4696235	1.00[JPT][hapmap]
rs4696237	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4696239	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4696648	1.00[JPT][hapmap]
rs6535763	1.00[JPT][hapmap]
rs6535765	1.00[JPT][hapmap]
rs6535766	1.00[JPT][hapmap]
rs6812695	1.00[JPT][hapmap]
rs6819599	1.00[JPT][hapmap]
rs6823953	1.00[JPT][hapmap]
rs6825613	1.00[JPT][hapmap]
rs6826863	1.00[JPT][hapmap]
rs6827056	0.83[ASN][1000 genomes]
rs6828937	1.00[JPT][hapmap]
rs6829963	1.00[JPT][hapmap]
rs6832257	0.83[ASN][1000 genomes]
rs6833956	1.00[JPT][hapmap]
rs6837905	1.00[JPT][hapmap]
rs6846323	0.85[ASN][1000 genomes]
rs6846981	0.85[ASN][1000 genomes]
rs6847934	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6853215	1.00[JPT][hapmap]
rs7439970	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7659146	1.00[JPT][hapmap]
rs7664483	0.83[ASN][1000 genomes]
rs7668154	1.00[JPT][hapmap]
rs7669180	0.83[ASN][1000 genomes]
rs7678748	1.00[JPT][hapmap]
rs7683092	1.00[JPT][hapmap]
rs7688786	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7690329	1.00[JPT][hapmap]
rs7691584	0.83[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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152096600-152118000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:152096800-152120600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:152097200-152123600	Weak transcription	Pancreas	Pancrea
4	chr4:152097200-152136600	Weak transcription	Colonic Mucosa	Colon
5	chr4:152097400-152123600	Weak transcription	Aorta	Aorta
6	chr4:152097600-152128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:152097800-152117200	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:152097800-152120000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:152098200-152117000	Weak transcription	Brain Anterior Caudate	brain
10	chr4:152098200-152118400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:152098400-152116600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:152098400-152118400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:152098400-152147200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:152100200-152116600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:152100600-152118000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:152106600-152115600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:152106600-152116600	Weak transcription	NHEK	skin
18	chr4:152106600-152117200	Weak transcription	Left Ventricle	heart
19	chr4:152106800-152116600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:152107200-152116000	Weak transcription	Ovary	ovary
21	chr4:152107200-152120000	Weak transcription	HepG2	liver
22	chr4:152107600-152116600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:152111800-152116600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:152112000-152117200	Weak transcription	Lung	lung
25	chr4:152112200-152116600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:152112200-152117200	Weak transcription	Right Atrium	heart
27	chr4:152112200-152120000	Weak transcription	Right Ventricle	heart
28	chr4:152112400-152117200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:152112400-152117200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:152112400-152120600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:152112600-152116000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:152112600-152117200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:152112600-152117400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:152112800-152120000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:152113400-152124400	Weak transcription	Fetal Intestine Small	intestine
36	chr4:152113600-152117200	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:152113800-152115800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:152114400-152117000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:152114400-152117000	Weak transcription	HSMM	muscle
40	chr4:152114400-152117200	Weak transcription	Brain Substantia Nigra	brain
41	chr4:152114800-152116600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:152114800-152116600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:152114800-152116600	Weak transcription	Adipose Nuclei	Adipose
44	chr4:152114800-152118200	Weak transcription	HSMMtube	muscle
45	chr4:152115000-152116600	Weak transcription	NHDF-Ad	bronchial
46	chr4:152115000-152117200	Weak transcription	Fetal Heart	heart
47	chr4:152115000-152117200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr4:152115000-152118200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr4:152115000-152124000	Weak transcription	Psoas Muscle	Psoas

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