Variant report

Variant	rs2542938
Chromosome Location	chr2:172413267-172413268
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172401705..172405203-chr2:172412295..172415295,3	K562	blood:
2	chr2:172376132..172377971-chr2:172413004..172415455,2	MCF-7	breast:
3	chr2:172411652..172413746-chr2:172420952..172422723,2	K562	blood:

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11682659	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11684782	0.83[JPT][hapmap]
rs13018808	0.89[CHB][hapmap];0.80[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2542933	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2542940	0.83[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs2674485	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528	0.85[AFR][1000 genomes]
rs6734880	0.83[ASN][1000 genomes]
rs7585194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2542938	CYBRD1	cis	Artery Aorta	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172386400-172419800	Weak transcription	Lung	lung
2	chr2:172387200-172413800	Weak transcription	Spleen	Spleen
3	chr2:172388800-172413800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:172388800-172413800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:172388800-172414800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:172388800-172414800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:172396600-172414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:172398200-172414000	Weak transcription	Brain Anterior Caudate	brain
9	chr2:172400000-172416400	Weak transcription	Gastric	stomach
10	chr2:172400200-172413800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:172406000-172413800	Weak transcription	Esophagus	oesophagus
12	chr2:172406200-172414400	Strong transcription	HSMMtube	muscle
13	chr2:172407200-172413600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:172407200-172414400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:172407600-172413400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:172408400-172414400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:172409200-172413600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:172410000-172415600	Weak transcription	NHEK	skin
19	chr2:172410400-172413400	Strong transcription	Left Ventricle	heart
20	chr2:172410400-172413600	Strong transcription	Adipose Nuclei	Adipose
21	chr2:172410400-172413600	Strong transcription	Fetal Muscle Leg	muscle
22	chr2:172410800-172413800	Weak transcription	Fetal Thymus	thymus
23	chr2:172410800-172415800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:172411000-172413600	Weak transcription	Placenta	Placenta
25	chr2:172411000-172414200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:172411200-172413600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:172411400-172414200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:172411800-172413800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:172411800-172415000	Weak transcription	K562	blood
30	chr2:172411800-172419000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:172412000-172414400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:172412000-172414400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:172412200-172413800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:172412200-172414600	Weak transcription	HSMM	muscle
35	chr2:172412200-172415000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:172412400-172413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:172412400-172414000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:172412400-172414000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:172412400-172414000	Weak transcription	NH-A	brain
40	chr2:172412400-172414800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr2:172412400-172415600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:172412400-172416000	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:172412400-172416400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:172412400-172417400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:172412600-172413600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:172412600-172413600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:172412600-172414600	Weak transcription	Fetal Stomach	stomach
48	chr2:172412600-172414800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:172412600-172415200	Weak transcription	Brain Substantia Nigra	brain
50	chr2:172412600-172415600	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links