Variant report

Variant	rs12239625
Chromosome Location	chr1:154924239-154924240
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	chr1:154922731..154925680-chr1:155022228..155024598,2	K562	blood:
2	chr1:154894734..154897695-chr1:154923296..154925878,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PYGO2-2	chr1:154923947-154924397	NONHSAT006648
2	lnc-PYGO2-2	chr1:154924113-154927297	NONHSAT006649

Variant related genes	Relation type
ENSG00000143537	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12064595	0.85[ASW][hapmap]
rs12078882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35981350	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7520378	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv872453	chr1:154904840-154995503	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription 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 miRNA target site	147 gene(s)	inside rSNPs	diseases
4	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154910400-154925000	Weak transcription	Psoas Muscle	Psoas
2	chr1:154910600-154927200	Weak transcription	Fetal Kidney	kidney
3	chr1:154910800-154927200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr1:154910800-154927200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:154911800-154927400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:154911800-154927400	Weak transcription	NHEK	skin
7	chr1:154913000-154927600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:154913200-154927400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:154913400-154925600	Weak transcription	Brain Germinal Matrix	brain
10	chr1:154913400-154927000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:154914000-154927400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:154914200-154927400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:154915200-154927400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:154916800-154927200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:154917200-154925200	Weak transcription	Small Intestine	intestine
16	chr1:154917200-154927200	Weak transcription	Hela-S3	cervix
17	chr1:154917600-154924400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:154917600-154924800	Weak transcription	Fetal Heart	heart
19	chr1:154917800-154924400	Weak transcription	K562	blood
20	chr1:154917800-154924600	Weak transcription	Right Atrium	heart
21	chr1:154917800-154925800	Weak transcription	Stomach Mucosa	stomach
22	chr1:154918600-154927800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:154919000-154924400	Strong transcription	Fetal Intestine Small	intestine
24	chr1:154919000-154926600	Weak transcription	Fetal Brain Female	brain
25	chr1:154919200-154924600	Strong transcription	Fetal Stomach	stomach
26	chr1:154919800-154927200	Weak transcription	NH-A	brain
27	chr1:154920600-154925000	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:154920800-154927200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:154921000-154925800	Weak transcription	Fetal Lung	lung
30	chr1:154921200-154925200	Weak transcription	Brain Angular Gyrus	brain
31	chr1:154922600-154924400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:154922600-154924400	Strong transcription	Fetal Muscle Leg	muscle
33	chr1:154922800-154924400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:154922800-154924400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:154922800-154924600	Strong transcription	Fetal Intestine Large	intestine
36	chr1:154922800-154924800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:154923000-154924400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:154923000-154924400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
39	chr1:154923000-154924400	Strong transcription	HSMMtube	muscle
40	chr1:154923000-154924600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:154923000-154924600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:154923000-154924600	Strong transcription	Gastric	stomach
43	chr1:154923000-154924600	Genic enhancers	Spleen	Spleen
44	chr1:154923000-154926800	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr1:154923200-154924800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:154923200-154925000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
47	chr1:154923200-154926200	Genic enhancers	Fetal Thymus	thymus
48	chr1:154923400-154924400	Genic enhancers	Thymus	Thymus
49	chr1:154923400-154926600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
50	chr1:154923600-154925000	Flanking Active TSS	GM12878-XiMat	blood

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