Variant report

Variant	rs2407165
Chromosome Location	chr4:152184146-152184147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10006188	1.00[ASN][1000 genomes]
rs10032413	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12509608	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12643490	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13134038	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134365	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1875308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280280	0.83[CHB][hapmap]
rs2280283	1.00[CEU][hapmap]
rs2407167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736502	1.00[CEU][hapmap]
rs4504229	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4529031	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6535764	1.00[CEU][hapmap]
rs6535778	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6835206	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845400	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6850311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7654306	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7656771	1.00[CEU][hapmap]
rs7668541	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152130200-152187800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:152149200-152185200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:152149200-152197600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:152165400-152189000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:152172800-152190600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:152173400-152189400	Weak transcription	Aorta	Aorta
7	chr4:152173800-152198200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:152174000-152187200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:152174000-152192200	Weak transcription	Brain Angular Gyrus	brain
10	chr4:152177400-152187600	Weak transcription	Fetal Intestine Large	intestine
11	chr4:152177400-152198200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:152177800-152200000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:152178200-152188200	Weak transcription	Liver	Liver
14	chr4:152180000-152193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:152180200-152189000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:152180800-152191000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:152181000-152184800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:152181000-152185000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr4:152182600-152189000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:152182600-152211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:152182800-152185200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr4:152182800-152206000	Weak transcription	NHEK	skin
23	chr4:152183000-152184200	Enhancers	Psoas Muscle	Psoas
24	chr4:152183200-152184800	Enhancers	Stomach Smooth Muscle	stomach
25	chr4:152183200-152198200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:152183400-152184400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:152183400-152184800	Enhancers	Colon Smooth Muscle	Colon
28	chr4:152183400-152184800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr4:152183400-152185000	Enhancers	Adipose Nuclei	Adipose
30	chr4:152183400-152185000	Enhancers	Fetal Heart	heart
31	chr4:152183400-152185000	Enhancers	Right Atrium	heart
32	chr4:152183400-152185000	Enhancers	Right Ventricle	heart
33	chr4:152183400-152185200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:152183400-152185200	Enhancers	Left Ventricle	heart
35	chr4:152183600-152184600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:152183600-152184600	Enhancers	Brain Substantia Nigra	brain
37	chr4:152183600-152185000	Enhancers	Brain Anterior Caudate	brain
38	chr4:152183600-152185000	Enhancers	Fetal Stomach	stomach
39	chr4:152183600-152185000	Enhancers	Ovary	ovary
40	chr4:152183600-152185200	Strong transcription	Fetal Intestine Small	intestine
41	chr4:152183600-152185200	Enhancers	Fetal Muscle Leg	muscle
42	chr4:152183800-152184400	Enhancers	Brain Hippocampus Middle	brain
43	chr4:152183800-152184400	Enhancers	Placenta Amnion	Placenta Amnion
44	chr4:152183800-152187000	Weak transcription	HepG2	liver
45	chr4:152184000-152184200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:152184000-152184200	Enhancers	Lung	lung
47	chr4:152184000-152184600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr4:152184000-152184800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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