Variant report

Variant	rs2619827
Chromosome Location	chr5:5475305-5475306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1004263	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10063885	0.81[EUR][1000 genomes]
rs1115068	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12653733	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541799	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2560297	0.83[EUR][1000 genomes]
rs2560298	0.81[EUR][1000 genomes]
rs2560299	0.82[EUR][1000 genomes]
rs2560300	0.82[EUR][1000 genomes]
rs2578500	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2578501	0.87[EUR][1000 genomes]
rs2578548	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2578549	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2578550	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2578552	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578553	0.83[EUR][1000 genomes]
rs2578554	0.83[EUR][1000 genomes]
rs2578556	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2578557	0.85[EUR][1000 genomes]
rs2578558	0.84[EUR][1000 genomes]
rs2578559	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578564	0.83[EUR][1000 genomes]
rs2578565	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2619844	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918253	0.84[EUR][1000 genomes]
rs2918260	0.82[EUR][1000 genomes]
rs2918261	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2964131	0.83[EUR][1000 genomes]
rs2964155	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2964159	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2964160	0.83[EUR][1000 genomes]
rs3097160	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3098377	0.83[EUR][1000 genomes]
rs61063822	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6894118	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757981	chr5:5447098-5764620	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv2759319	chr5:5447098-5764620	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5430200-5478800	Weak transcription	Stomach Mucosa	stomach
2	chr5:5433400-5495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:5436600-5478200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:5437200-5477000	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:5437400-5480000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:5442400-5475800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:5458600-5495000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:5460000-5481600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:5462400-5494600	Weak transcription	Colonic Mucosa	Colon
10	chr5:5463000-5493800	Weak transcription	Fetal Heart	heart
11	chr5:5463400-5480800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:5463800-5483600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:5464400-5476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:5464800-5475600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr5:5465000-5475800	Weak transcription	Pancreas	Pancrea
16	chr5:5465200-5475800	Weak transcription	Lung	lung
17	chr5:5465200-5476600	Weak transcription	Spleen	Spleen
18	chr5:5465200-5482600	Weak transcription	Gastric	stomach
19	chr5:5465200-5493800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:5465200-5495000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:5465400-5476600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:5466400-5475600	Weak transcription	NHDF-Ad	bronchial
23	chr5:5467000-5476400	Weak transcription	Brain Germinal Matrix	brain
24	chr5:5467600-5488800	Weak transcription	Brain Substantia Nigra	brain
25	chr5:5468000-5494000	Weak transcription	Fetal Brain Male	brain
26	chr5:5468400-5476600	Weak transcription	Psoas Muscle	Psoas
27	chr5:5468400-5480800	Weak transcription	NHEK	skin
28	chr5:5468800-5479600	Weak transcription	K562	blood
29	chr5:5470400-5492600	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:5471800-5476600	Strong transcription	Primary B cells from cord blood	blood
31	chr5:5472000-5479200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:5472000-5480200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:5472200-5477000	Strong transcription	Hela-S3	cervix
34	chr5:5472200-5478400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:5472400-5477200	Strong transcription	HSMM	muscle
36	chr5:5472400-5478200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr5:5472400-5478600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:5472600-5477200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr5:5472600-5477200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr5:5472600-5479000	Strong transcription	Adipose Nuclei	Adipose
41	chr5:5472600-5479200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:5472600-5480200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:5472800-5477000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr5:5472800-5477400	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr5:5472800-5478200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr5:5472800-5490600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:5473000-5476800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr5:5473000-5477000	Strong transcription	HUVEC	blood vessel
49	chr5:5473000-5477600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr5:5473000-5478200	Strong transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links