Variant report

Variant	rs12062984
Chromosome Location	chr1:153737326-153737327
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153737056-153737557	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153614249..153616025-chr1:153735585..153737943,2	K562	blood:
2	chr1:153660375..153662703-chr1:153735241..153738105,2	K562	blood:
3	chr1:153710268..153712803-chr1:153735091..153737564,2	K562	blood:

Variant related genes	Relation type
INTS3	TF binding region
ENSG00000169418	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12065984	1.00[AFR][1000 genomes]
rs7548743	1.00[MEX][hapmap]
rs9725547	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153712600-153741400	Strong transcription	Placenta	Placenta
2	chr1:153712800-153737800	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr1:153712800-153737800	Strong transcription	Placenta Amnion	Placenta Amnion
4	chr1:153712800-153738000	Strong transcription	Fetal Brain Female	brain
5	chr1:153712800-153738200	Strong transcription	Thymus	Thymus
6	chr1:153712800-153742800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr1:153712800-153743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:153712800-153744800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:153712800-153746400	Strong transcription	Brain Germinal Matrix	brain
10	chr1:153712800-153751800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:153713000-153738200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:153713000-153738600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:153713000-153745400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:153713000-153745400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:153713000-153746400	Strong transcription	Primary T cells from cord blood	blood
16	chr1:153713000-153747000	Strong transcription	Dnd41	blood
17	chr1:153714000-153746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:153715200-153738000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:153715400-153745600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:153715600-153745600	Strong transcription	Fetal Thymus	thymus
21	chr1:153716400-153746000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:153719800-153746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:153721000-153738200	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr1:153722000-153743800	Strong transcription	Fetal Stomach	stomach
25	chr1:153722200-153738000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:153722200-153742800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr1:153722400-153738200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:153722400-153743000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:153722400-153746200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:153722400-153746800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:153722600-153742800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:153722600-153746600	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr1:153722800-153738200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:153722800-153742800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:153723600-153746800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:153723800-153740800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:153724000-153738000	Strong transcription	GM12878-XiMat	blood
38	chr1:153724000-153740200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:153725600-153747200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:153726400-153746200	Strong transcription	Fetal Lung	lung
41	chr1:153726800-153746000	Strong transcription	Ovary	ovary
42	chr1:153727400-153739200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:153727800-153746400	Weak transcription	Fetal Heart	heart
44	chr1:153728400-153745800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:153728800-153737800	Strong transcription	Hela-S3	cervix
46	chr1:153729200-153740400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:153729400-153737800	Strong transcription	HMEC	breast
48	chr1:153729400-153738000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:153729400-153738200	Strong transcription	Aorta	Aorta
50	chr1:153729400-153743200	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links