Variant report

Variant	rs1539725
Chromosome Location	chr1:193153682-193153683
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	chr1:193091690..193093803-chr1:193152706..193155451,2	K562	blood:
2	chr1:193146146..193149331-chr1:193151416..193154903,3	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10754051	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10921309	0.87[ASW][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs10921327	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6428156	0.82[CHD][hapmap]
rs6661522	0.87[CHD][hapmap];0.95[JPT][hapmap]
rs6697079	0.81[CHD][hapmap]

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	nsv832148	chr1:193143945-193292897	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv872831	chr1:193152317-193322087	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1539725	B3GALT2	cis	cerebellum	SCAN
rs1539725	CDC73	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:193094800-193155000	Weak transcription	Aorta	Aorta
2	chr1:193110000-193155200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:193121000-193155200	Weak transcription	Pancreas	Pancrea
4	chr1:193123400-193155200	Weak transcription	Thymus	Thymus
5	chr1:193124000-193154200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:193126200-193154400	Weak transcription	NHEK	skin
7	chr1:193126200-193155200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:193126200-193155200	Weak transcription	Gastric	stomach
9	chr1:193126800-193155000	Weak transcription	Fetal Thymus	thymus
10	chr1:193127600-193154400	Weak transcription	Hela-S3	cervix
11	chr1:193128600-193154800	Weak transcription	NH-A	brain
12	chr1:193130400-193154800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:193131800-193158600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:193133200-193154800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:193133200-193154800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:193134000-193154400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:193135600-193155000	Weak transcription	Small Intestine	intestine
18	chr1:193135600-193155200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:193137600-193154400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:193137600-193154800	Weak transcription	HMEC	breast
21	chr1:193140200-193154800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:193140400-193155200	Weak transcription	Adipose Nuclei	Adipose
23	chr1:193140400-193159800	Weak transcription	Dnd41	blood
24	chr1:193140600-193154800	Weak transcription	HUVEC	blood vessel
25	chr1:193140600-193155200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:193140800-193154000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:193140800-193161400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr1:193142000-193154400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:193142200-193155400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:193142400-193154600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:193142800-193155200	Weak transcription	GM12878-XiMat	blood
32	chr1:193144200-193160400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:193144600-193155400	Weak transcription	Primary B cells from cord blood	blood
34	chr1:193147800-193155000	Weak transcription	Primary T cells from cord blood	blood
35	chr1:193148400-193161200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:193149600-193156600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:193149800-193156600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr1:193150000-193155000	Weak transcription	K562	blood
39	chr1:193150200-193156400	Active TSS	Brain Angular Gyrus	brain
40	chr1:193150400-193157600	Active TSS	Fetal Brain Female	brain
41	chr1:193150800-193154000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:193150800-193154800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:193150800-193156000	Active TSS	Fetal Brain Male	brain
44	chr1:193150800-193156000	Active TSS	HSMM	muscle
45	chr1:193150800-193157000	Active TSS	HSMMtube	muscle
46	chr1:193151200-193154200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:193151400-193155000	Active TSS	Fetal Lung	lung
48	chr1:193151400-193155000	Weak transcription	Left Ventricle	heart
49	chr1:193151400-193155000	Weak transcription	Psoas Muscle	Psoas
50	chr1:193151400-193155000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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