Variant report

Variant	rs59356309
Chromosome Location	chr2:48709315-48709316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10209255	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11125173	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12618125	0.80[EUR][1000 genomes]
rs34461314	0.83[EUR][1000 genomes]
rs35913553	0.93[AMR][1000 genomes]
rs4073573	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4131784	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4528813	0.86[EUR][1000 genomes]
rs4549145	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4641991	0.86[EUR][1000 genomes]
rs4953587	0.86[EUR][1000 genomes]
rs6545047	0.84[EUR][1000 genomes]
rs6754946	0.84[EUR][1000 genomes]
rs72822226	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72822230	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59356309	CCDC128	Cis_1M	lymphoblastoid	RTeQTL
rs59356309	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48673200-48724000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:48682600-48716200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:48689200-48735600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:48690000-48735600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:48694000-48729400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:48694200-48753000	Weak transcription	Psoas Muscle	Psoas
7	chr2:48695200-48709800	Weak transcription	NHLF	lung
8	chr2:48695200-48723800	Weak transcription	Gastric	stomach
9	chr2:48695200-48725800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:48695200-48728000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:48695400-48728000	Weak transcription	Hela-S3	cervix
12	chr2:48695600-48713400	Weak transcription	Colonic Mucosa	Colon
13	chr2:48695600-48735200	Weak transcription	K562	blood
14	chr2:48696200-48721000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:48696400-48710000	Weak transcription	Lung	lung
16	chr2:48696400-48716400	Weak transcription	Right Ventricle	heart
17	chr2:48696400-48721600	Weak transcription	Left Ventricle	heart
18	chr2:48696400-48723800	Weak transcription	Aorta	Aorta
19	chr2:48698600-48723200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:48698800-48710600	Weak transcription	NHEK	skin
21	chr2:48698800-48711000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:48698800-48729200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:48698800-48735400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:48700200-48735400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:48700600-48718400	Strong transcription	Primary T cells from cord blood	blood
26	chr2:48700600-48735600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:48701600-48709800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:48701600-48714400	Strong transcription	GM12878-XiMat	blood
29	chr2:48701800-48715000	Weak transcription	NHDF-Ad	bronchial
30	chr2:48702000-48716400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:48702400-48709400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:48703200-48723400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:48703200-48729800	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:48704000-48712400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:48704000-48718600	Strong transcription	Fetal Thymus	thymus
36	chr2:48704000-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:48704200-48709400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:48704200-48716800	Strong transcription	Placenta	Placenta
39	chr2:48704400-48718600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:48704400-48730000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr2:48704600-48717000	Strong transcription	Primary B cells from cord blood	blood
42	chr2:48704600-48735400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr2:48704600-48735600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr2:48704800-48710200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:48704800-48711600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:48705000-48710800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:48705000-48711400	Strong transcription	Dnd41	blood
48	chr2:48705400-48713600	Weak transcription	HSMM	muscle
49	chr2:48705400-48716200	Weak transcription	Esophagus	oesophagus
50	chr2:48705600-48712000	Enhancers	Rectal Smooth Muscle	rectum

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