Variant report

Variant	rs2541009
Chromosome Location	chr2:37290659-37290660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37288334..37292049-chr2:37300310..37302436,3	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1060957	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17020213	0.88[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs17445820	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17498825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253629	0.88[CEU][hapmap];0.81[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs2540992	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2541008	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3856499	0.90[ASN][1000 genomes]
rs66476568	0.98[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv873879	chr2:37200033-37299145	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv581472	chr2:37235324-37291320	Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2541009	CEBPZ	cis	cerebellum	SCAN
rs2541009	CCDC75	Cis_1M	lymphoblastoid	RTeQTL
rs2541009	CEBPZ	cis	lymphoblastoid	seeQTL
rs2541009	EIF2AK2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37221000-37307600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:37223400-37300400	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr2:37240400-37304800	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr2:37240600-37306000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:37240800-37306400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:37240800-37307000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:37241200-37306000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:37241400-37299600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:37242200-37305800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:37249000-37291800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:37249000-37291800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:37253800-37291000	Weak transcription	Aorta	Aorta
13	chr2:37253800-37310200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:37258400-37291800	Weak transcription	Esophagus	oesophagus
15	chr2:37266200-37291800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:37272400-37306400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:37272600-37293800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:37272600-37299400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:37272600-37309800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:37274200-37308800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:37274400-37299200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:37274400-37309600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:37275000-37294800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr2:37275200-37300200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr2:37275200-37307000	Strong transcription	Adipose Nuclei	Adipose
26	chr2:37275400-37299400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:37275400-37309200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:37276400-37296800	Strong transcription	Osteobl	bone
29	chr2:37276800-37299400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:37277000-37291800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:37277600-37299400	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:37278000-37299600	Strong transcription	Liver	Liver
33	chr2:37278600-37297600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:37278600-37310800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:37279200-37293200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:37279200-37294000	Strong transcription	NH-A	brain
37	chr2:37279200-37300200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr2:37279200-37309200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:37279400-37307600	Strong transcription	Fetal Intestine Large	intestine
40	chr2:37280000-37291800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:37280000-37291800	Weak transcription	Gastric	stomach
42	chr2:37281000-37291400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:37281800-37307200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:37282000-37293200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:37282000-37308400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:37282800-37296600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:37284600-37291800	Weak transcription	NHEK	skin
48	chr2:37284600-37307200	Weak transcription	Stomach Mucosa	stomach
49	chr2:37284800-37291200	Weak transcription	Fetal Kidney	kidney
50	chr2:37285600-37291600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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