Variant report

Variant	rs12072899
Chromosome Location	chr1:241679474-241679475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241616113..241618649-chr1:241678883..241680666,2	K562	blood:
2	chr1:241677220..241680834-chr1:241684726..241688550,4	K562	blood:
3	chr1:241654504..241656882-chr1:241679445..241682289,2	K562	blood:
4	chr1:241678718..241680701-chr1:241800665..241802574,2	K562	blood:
5	chr1:241657615..241659200-chr1:241678785..241681032,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10926501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12075678	1.00[AMR][1000 genomes]
rs2070080	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs598292	1.00[MEX][hapmap]
rs615141	1.00[MEX][hapmap]
rs643321	1.00[MEX][hapmap]
rs9428514	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv873371	chr1:241667244-241747838	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241657000-241680000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:241657400-241680000	Strong transcription	Primary B cells from cord blood	blood
3	chr1:241659000-241682000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:241659200-241679800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:241661200-241681400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:241664800-241680600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:241665000-241679600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:241667400-241680800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:241667400-241681800	Weak transcription	Fetal Brain Male	brain
10	chr1:241667600-241681800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:241667800-241682000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:241668000-241679600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:241668000-241680600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:241668000-241682000	Weak transcription	Pancreas	Pancrea
15	chr1:241668000-241682200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:241668000-241682200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:241668000-241682200	Weak transcription	Esophagus	oesophagus
18	chr1:241668800-241680400	Weak transcription	Fetal Stomach	stomach
19	chr1:241670000-241679800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:241671600-241679800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:241671800-241679800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:241671800-241679800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr1:241671800-241682000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:241672000-241681200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:241672000-241681200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:241672000-241681200	Weak transcription	Stomach Mucosa	stomach
27	chr1:241672000-241681400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:241672000-241682000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:241672200-241681800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:241672800-241681200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:241673200-241682200	Weak transcription	Spleen	Spleen
32	chr1:241674800-241681400	Weak transcription	Thymus	Thymus
33	chr1:241674800-241681800	Weak transcription	Small Intestine	intestine
34	chr1:241674800-241682000	Weak transcription	Colonic Mucosa	Colon
35	chr1:241675200-241681400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:241675400-241681800	Weak transcription	Ovary	ovary
37	chr1:241675600-241681400	Weak transcription	HSMMtube	muscle
38	chr1:241675600-241681800	Weak transcription	Brain Germinal Matrix	brain
39	chr1:241675800-241679600	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:241675800-241679600	Weak transcription	Gastric	stomach
41	chr1:241675800-241680600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:241675800-241680600	Weak transcription	Colon Smooth Muscle	Colon
43	chr1:241675800-241680600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:241675800-241680800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:241675800-241680800	Weak transcription	Fetal Kidney	kidney
46	chr1:241675800-241681200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:241675800-241681200	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:241675800-241681400	Weak transcription	Brain Angular Gyrus	brain
49	chr1:241675800-241681800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:241675800-241681800	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links