Variant report

Variant	rs55721088
Chromosome Location	chr5:127858923-127858924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10039900	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10042096	0.97[ASN][1000 genomes]
rs10053025	0.97[ASN][1000 genomes]
rs10062344	0.81[ASN][1000 genomes]
rs10063362	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10477685	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10478812	0.92[ASN][1000 genomes]
rs10478813	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10478814	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11960575	0.92[ASN][1000 genomes]
rs17164094	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17164113	0.97[ASN][1000 genomes]
rs17839642	0.91[ASN][1000 genomes]
rs1897998	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55735252	0.81[ASN][1000 genomes]
rs56049336	0.92[ASN][1000 genomes]
rs57050667	0.97[ASN][1000 genomes]
rs58889726	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59674940	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60201468	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60571728	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60975118	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6595830	0.97[ASN][1000 genomes]
rs6595831	0.97[ASN][1000 genomes]
rs6595834	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6595836	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6595837	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6860199	0.97[ASN][1000 genomes]
rs6864057	0.94[ASN][1000 genomes]
rs6886186	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6887851	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6892484	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6893116	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6893181	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6893248	0.81[ASN][1000 genomes]
rs6893301	0.81[ASN][1000 genomes]
rs73346331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73784600	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73787623	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73787627	0.81[ASN][1000 genomes]
rs768744	0.95[ASN][1000 genomes]
rs7703313	0.92[ASN][1000 genomes]
rs7708713	0.97[ASN][1000 genomes]
rs7713044	0.97[ASN][1000 genomes]
rs7722917	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7722950	0.97[ASN][1000 genomes]
rs7723500	0.97[ASN][1000 genomes]
rs7725740	0.97[ASN][1000 genomes]
rs7726535	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9327478	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs981411	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv1015650	chr5:127745955-127866566	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
3	esv2763497	chr5:127745955-127882468	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv530822	chr5:127777365-127900742	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv427734	chr5:127805281-128088632	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1019560	chr5:127814656-127873680	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv537895	chr5:127814656-127873680	ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127826200-127859800	Weak transcription	NH-A	brain
2	chr5:127827200-127870400	Weak transcription	Fetal Kidney	kidney
3	chr5:127840200-127859600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:127840200-127870400	Weak transcription	Left Ventricle	heart
5	chr5:127840200-127872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:127840400-127864200	Weak transcription	Fetal Intestine Large	intestine
7	chr5:127840400-127867600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:127841000-127859600	Weak transcription	NHEK	skin
9	chr5:127841000-127870200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:127842600-127863600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:127844200-127860000	Weak transcription	Fetal Lung	lung
12	chr5:127845600-127867800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:127845600-127870400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:127846000-127867800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:127847400-127862200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:127847400-127869000	Weak transcription	NHDF-Ad	bronchial
17	chr5:127852400-127860000	Weak transcription	A549	lung
18	chr5:127852800-127867800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:127853200-127861000	Strong transcription	Placenta	Placenta
20	chr5:127853200-127872400	Weak transcription	Osteobl	bone
21	chr5:127853400-127864800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:127853400-127867600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:127853600-127867800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:127853800-127859800	Strong transcription	Fetal Muscle Leg	muscle
25	chr5:127853800-127862800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:127854000-127872000	Weak transcription	Ovary	ovary
27	chr5:127854600-127860600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:127854800-127859400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:127855000-127862000	Weak transcription	HUVEC	blood vessel
30	chr5:127855000-127863600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:127855000-127867600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:127855000-127871200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:127855400-127867800	Weak transcription	Fetal Stomach	stomach
34	chr5:127856000-127862400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:127856200-127859400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:127856400-127859600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:127856600-127859400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:127856600-127860000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:127856600-127860000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr5:127857000-127859800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr5:127857400-127859000	Enhancers	Primary hematopoietic stem cells	blood
42	chr5:127857400-127859400	Enhancers	Primary T cells from cord blood	blood
43	chr5:127857800-127869200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:127858200-127859800	Enhancers	Fetal Heart	heart
45	chr5:127858200-127860200	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr5:127858200-127861800	Weak transcription	HMEC	breast
47	chr5:127858200-127862000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:127858400-127859200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:127858600-127863200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:127858600-127864600	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links