Variant report

Variant	rs2407415
Chromosome Location	chr4:152133153-152133154
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10000557	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10001039	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10005907	0.90[ASN][1000 genomes]
rs10011421	0.83[ASN][1000 genomes]
rs10016998	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10017154	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10030785	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10032477	0.85[ASN][1000 genomes]
rs10213332	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046168	0.85[ASN][1000 genomes]
rs10776521	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10776523	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857254	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10857255	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857256	0.90[ASN][1000 genomes]
rs10964	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11099783	0.85[ASN][1000 genomes]
rs11099787	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11099788	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11099790	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11099791	0.93[ASN][1000 genomes]
rs11099794	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099795	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723219	0.85[ASN][1000 genomes]
rs11726180	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11729981	1.00[ASN][1000 genomes]
rs11730087	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734586	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11938266	0.85[ASN][1000 genomes]
rs11943477	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12500168	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12500223	1.00[ASN][1000 genomes]
rs12507657	0.85[ASN][1000 genomes]
rs13123932	0.90[ASN][1000 genomes]
rs13148755	0.81[ASN][1000 genomes]
rs13149045	1.00[ASN][1000 genomes]
rs1316364	1.00[ASN][1000 genomes]
rs1320006	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320007	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320192	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878796	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407406	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407411	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407414	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407424	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407425	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407426	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407427	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407428	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407429	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407430	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407439	0.85[ASN][1000 genomes]
rs2407440	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407441	0.81[ASN][1000 genomes]
rs2897657	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897660	0.88[ASN][1000 genomes]
rs4434229	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4616734	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640649	0.83[ASN][1000 genomes]
rs4696229	0.83[ASN][1000 genomes]
rs4696235	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696237	1.00[ASN][1000 genomes]
rs6535766	0.85[ASN][1000 genomes]
rs6535767	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6535775	0.95[ASN][1000 genomes]
rs6535776	1.00[ASN][1000 genomes]
rs6535777	0.81[ASN][1000 genomes]
rs6812695	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6815608	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6823953	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825613	0.88[ASN][1000 genomes]
rs6825952	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6828937	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829963	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6837905	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6838301	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838845	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847669	1.00[ASN][1000 genomes]
rs6853215	0.85[ASN][1000 genomes]
rs6856569	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7659146	0.85[ASN][1000 genomes]
rs7666751	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668154	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7681030	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7683092	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7687117	1.00[ASN][1000 genomes]
rs7689095	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7690329	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695005	1.00[ASN][1000 genomes]
rs938990	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152097200-152136600	Weak transcription	Colonic Mucosa	Colon
2	chr4:152098400-152147200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:152117600-152148800	Weak transcription	Esophagus	oesophagus
4	chr4:152118800-152146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:152119000-152139400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:152119400-152139400	Weak transcription	NHEK	skin
7	chr4:152120800-152153800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:152121000-152136400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:152121000-152138000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:152121200-152133800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:152124400-152136400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:152124400-152139600	Weak transcription	Osteobl	bone
13	chr4:152124400-152147000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:152124600-152136200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:152124600-152139400	Weak transcription	HSMM	muscle
16	chr4:152124600-152139600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:152124600-152139800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:152124600-152146800	Weak transcription	HSMMtube	muscle
19	chr4:152124800-152136400	Weak transcription	NH-A	brain
20	chr4:152124800-152140000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:152126400-152147200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:152126800-152147000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:152127200-152136400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:152128000-152140600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:152128000-152141600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:152128400-152138000	Weak transcription	Fetal Stomach	stomach
27	chr4:152128400-152139600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:152128400-152146600	Weak transcription	HMEC	breast
29	chr4:152128400-152146800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:152128600-152147200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:152129000-152136200	Weak transcription	Left Ventricle	heart
32	chr4:152129000-152139200	Weak transcription	NHDF-Ad	bronchial
33	chr4:152129000-152139600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:152129000-152146800	Weak transcription	Brain Angular Gyrus	brain
35	chr4:152129000-152148800	Weak transcription	Fetal Intestine Large	intestine
36	chr4:152129000-152168000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:152129200-152133600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:152129200-152136400	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:152129200-152136600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:152129200-152136800	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:152129200-152138400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr4:152129200-152142200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr4:152129200-152148800	Weak transcription	Liver	Liver
44	chr4:152129400-152133400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:152129400-152133600	Weak transcription	Adipose Nuclei	Adipose
46	chr4:152129400-152134000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:152129400-152136200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:152129400-152136600	Weak transcription	Brain Substantia Nigra	brain
49	chr4:152129400-152143800	Weak transcription	Fetal Intestine Small	intestine
50	chr4:152129400-152167800	Weak transcription	Right Ventricle	heart

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