Variant report

Variant	rs28628106
Chromosome Location	chr4:106607241-106607242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10516523	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11722731	0.92[ASN][1000 genomes]
rs11933386	0.81[EUR][1000 genomes]
rs11934139	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11941690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639750	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1294667	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1294669	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1294670	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1294673	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13120110	0.82[EUR][1000 genomes]
rs13147012	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13148869	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17036098	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17262764	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2080789	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544395	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544398	0.81[EUR][1000 genomes]
rs2544404	0.81[EUR][1000 genomes]
rs2544405	0.81[EUR][1000 genomes]
rs2544412	0.82[EUR][1000 genomes]
rs2544413	0.85[EUR][1000 genomes]
rs2553432	0.81[EUR][1000 genomes]
rs2553436	0.81[EUR][1000 genomes]
rs2553438	0.80[EUR][1000 genomes]
rs2553441	0.81[EUR][1000 genomes]
rs2553449	0.84[ASN][1000 genomes]
rs2553458	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2553462	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2553468	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756260	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4699196	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6533218	0.85[EUR][1000 genomes]
rs6820200	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7680134	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7684442	0.85[AMR][1000 genomes]
rs7684839	0.89[ASN][1000 genomes]
rs7685231	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106580400-106613200	Weak transcription	Fetal Intestine Small	intestine
2	chr4:106587800-106629000	Weak transcription	Lung	lung
3	chr4:106597000-106610000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:106598600-106613000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:106599000-106614400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:106599200-106613800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:106600400-106628600	Weak transcription	Colonic Mucosa	Colon
8	chr4:106600600-106628400	Weak transcription	Stomach Mucosa	stomach
9	chr4:106601200-106609600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:106601200-106628400	Weak transcription	Psoas Muscle	Psoas
11	chr4:106601600-106609200	Weak transcription	A549	lung
12	chr4:106601800-106612600	Weak transcription	Fetal Brain Female	brain
13	chr4:106602000-106618600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:106602200-106621600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:106602200-106629200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:106602400-106610800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:106602400-106613200	Weak transcription	Fetal Stomach	stomach
18	chr4:106602400-106615400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:106602400-106618400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:106602400-106621600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr4:106602400-106628600	Weak transcription	Right Ventricle	heart
22	chr4:106602600-106607800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:106602600-106608200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:106602600-106609200	Weak transcription	Fetal Brain Male	brain
25	chr4:106602600-106609200	Weak transcription	K562	blood
26	chr4:106602600-106609600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:106602600-106610600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:106602600-106611200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:106602600-106611600	Strong transcription	Adipose Nuclei	Adipose
30	chr4:106602600-106614000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:106602600-106614000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:106602600-106620800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:106602600-106621200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:106602600-106621800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:106602600-106622200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr4:106602600-106628400	Weak transcription	Fetal Heart	heart
37	chr4:106602600-106629200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:106602800-106607600	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:106602800-106608200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:106602800-106612000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:106602800-106614400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:106602800-106617200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr4:106602800-106619200	Strong transcription	Liver	Liver
44	chr4:106603000-106617200	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr4:106603000-106620200	Strong transcription	Placenta	Placenta
46	chr4:106603000-106620400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr4:106603000-106620400	Strong transcription	Dnd41	blood
48	chr4:106603000-106621000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:106603600-106607600	Strong transcription	HUVEC	blood vessel
50	chr4:106603600-106611400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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