Variant report

Variant	rs2407413
Chromosome Location	chr4:152139574-152139575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10016092	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10020297	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10434137	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10461254	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10461255	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10520101	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10520102	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10776522	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11099792	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099793	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099796	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11945206	0.91[ASN][1000 genomes]
rs12644496	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12647306	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13103344	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13111753	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13122609	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13125574	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2407222	0.91[ASN][1000 genomes]
rs2407223	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2407407	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407408	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407409	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407410	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407412	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407417	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407418	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2897655	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2897656	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4266274	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4312738	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4467540	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4591577	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4696234	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696239	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6847934	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7439970	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7688786	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[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	chr4:152098400-152147200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:152117600-152148800	Weak transcription	Esophagus	oesophagus
3	chr4:152118800-152146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:152120800-152153800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:152124400-152139600	Weak transcription	Osteobl	bone
6	chr4:152124400-152147000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:152124600-152139600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:152124600-152139800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:152124600-152146800	Weak transcription	HSMMtube	muscle
10	chr4:152124800-152140000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:152126400-152147200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:152126800-152147000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:152128000-152140600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:152128000-152141600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:152128400-152139600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:152128400-152146600	Weak transcription	HMEC	breast
17	chr4:152128400-152146800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:152128600-152147200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:152129000-152139600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:152129000-152146800	Weak transcription	Brain Angular Gyrus	brain
21	chr4:152129000-152148800	Weak transcription	Fetal Intestine Large	intestine
22	chr4:152129000-152168000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:152129200-152142200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:152129200-152148800	Weak transcription	Liver	Liver
25	chr4:152129400-152143800	Weak transcription	Fetal Intestine Small	intestine
26	chr4:152129400-152167800	Weak transcription	Right Ventricle	heart
27	chr4:152129600-152140200	Weak transcription	HepG2	liver
28	chr4:152129600-152146800	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:152129600-152147200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:152130200-152187800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:152133600-152147200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:152134400-152139600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:152136200-152139600	Enhancers	HUVEC	blood vessel
34	chr4:152136400-152139800	Enhancers	Fetal Lung	lung
35	chr4:152136400-152140400	Enhancers	Adipose Nuclei	Adipose
36	chr4:152136600-152158000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:152137000-152144400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:152137000-152145600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:152137000-152145800	Weak transcription	NH-A	brain
40	chr4:152137000-152146800	Weak transcription	Brain Substantia Nigra	brain
41	chr4:152137000-152147400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:152137200-152143800	Weak transcription	Right Atrium	heart
43	chr4:152137400-152146800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:152137400-152147200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:152137400-152148800	Weak transcription	Left Ventricle	heart
46	chr4:152137600-152146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:152138600-152140400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:152138800-152142400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr4:152138800-152146800	Weak transcription	Fetal Stomach	stomach
50	chr4:152139000-152142200	Weak transcription	Colon Smooth Muscle	Colon

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