Variant report

Variant	rs560494
Chromosome Location	chr2:169733043-169733044
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:169728195..169733629-chr2:169741403..169748359,8	K562	blood:

Variant related genes	Relation type
ENSG00000152253	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10084216	0.87[AFR][1000 genomes]
rs16856052	1.00[YRI][hapmap]
rs2685800	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2685801	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475467	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs477309	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs479661	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494859	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs498041	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs499160	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs504393	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs509988	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511778	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs525428	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs533492	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534771	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs539400	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576338	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs577192	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs580507	0.92[EUR][1000 genomes]
rs581363	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[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	nsv583599	chr2:169664227-169903096	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv875381	chr2:169686559-169749841	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169698600-169744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:169709800-169733400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:169715400-169746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:169716000-169745800	Weak transcription	HSMM	muscle
5	chr2:169717000-169746400	Weak transcription	Primary B cells from cord blood	blood
6	chr2:169719800-169733600	Weak transcription	NHDF-Ad	bronchial
7	chr2:169722000-169736200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:169722000-169741200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:169722000-169741400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:169722000-169741400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:169722000-169741400	Weak transcription	NHEK	skin
12	chr2:169722000-169741800	Weak transcription	Fetal Lung	lung
13	chr2:169722000-169742800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:169722000-169744000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:169722000-169745800	Weak transcription	Fetal Stomach	stomach
16	chr2:169722000-169745800	Weak transcription	GM12878-XiMat	blood
17	chr2:169722000-169746000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:169722000-169746000	Weak transcription	Fetal Intestine Large	intestine
19	chr2:169722000-169746000	Weak transcription	Fetal Intestine Small	intestine
20	chr2:169722000-169746000	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:169722200-169741400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:169724000-169733200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:169727600-169733800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:169728000-169733800	Strong transcription	K562	blood
25	chr2:169728000-169734000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr2:169728200-169734000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:169728600-169733200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:169728600-169741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:169729000-169736400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:169729200-169733200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:169729600-169741600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:169729600-169745800	Weak transcription	Thymus	Thymus
33	chr2:169730000-169736400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:169730000-169741400	Weak transcription	HMEC	breast
35	chr2:169730200-169733200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:169730200-169740800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:169730200-169743200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:169730200-169745800	Weak transcription	HUVEC	blood vessel
39	chr2:169730400-169733400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:169730400-169740600	Weak transcription	HepG2	liver
41	chr2:169730400-169741000	Weak transcription	A549	lung
42	chr2:169730600-169734000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:169731200-169740000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:169731600-169746200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:169731800-169736200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:169731800-169741400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr2:169731800-169741600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:169731800-169746600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:169732000-169745800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:169732200-169738800	Weak transcription	Fetal Thymus	thymus

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