Variant report

Variant	rs12170576
Chromosome Location	chr22:30716956-30716957
allele	C/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	TAL1	chr22:30716891-30717256	K562	blood:	n/a	chr22:30717117-30717126 chr22:30717053-30717071

No.	Distal block	Cell Line	Cell type
1	chr22:30716894..30719257-chr22:30719729..30722601,2	MCF-7	breast:
2	chr22:30715065..30719307-chr22:30719404..30722412,5	K562	blood:
3	chr22:30715105..30720415-chr22:30721123..30724883,5	MCF-7	breast:
4	chr22:30672847..30675715-chr22:30716721..30718257,2	MCF-7	breast:
5	chr22:30715065..30718690-chr22:30719404..30722127,4	K562	blood:

Variant related genes	Relation type
TBC1D10A	TF binding region
ENSG00000099992	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12165697	0.87[AMR][1000 genomes]
rs12165816	0.87[AMR][1000 genomes]
rs12166309	0.87[AMR][1000 genomes]
rs12166660	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12167903	1.00[AMR][1000 genomes]
rs12168516	0.83[AFR][1000 genomes]
rs12170269	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9619106	1.00[AMR][1000 genomes]
rs9620980	0.87[AMR][1000 genomes]
rs9653824	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv984527	chr22:30698358-30732712	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv3593	chr22:30705980-30751122	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30686200-30720000	Weak transcription	Fetal Brain Male	brain
2	chr22:30705000-30720400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr22:30706000-30719400	Genic enhancers	Dnd41	blood
4	chr22:30706200-30720000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr22:30706600-30720400	Genic enhancers	Fetal Thymus	thymus
6	chr22:30707400-30720800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr22:30707800-30720400	Weak transcription	Fetal Lung	lung
8	chr22:30707800-30720800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr22:30709000-30717600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr22:30709200-30717400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr22:30709600-30720600	Strong transcription	Fetal Stomach	stomach
12	chr22:30710000-30717400	Weak transcription	Brain Anterior Caudate	brain
13	chr22:30710200-30719800	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr22:30710400-30720800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr22:30710400-30720800	Weak transcription	Fetal Kidney	kidney
16	chr22:30710600-30720400	Weak transcription	Brain Hippocampus Middle	brain
17	chr22:30710800-30718000	Enhancers	Ovary	ovary
18	chr22:30710800-30718400	Strong transcription	Fetal Intestine Small	intestine
19	chr22:30711000-30717800	Weak transcription	Brain Angular Gyrus	brain
20	chr22:30711200-30720200	Weak transcription	Small Intestine	intestine
21	chr22:30711400-30719400	Weak transcription	NH-A	brain
22	chr22:30711800-30717000	Weak transcription	K562	blood
23	chr22:30711800-30721200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr22:30712000-30721000	Weak transcription	A549	lung
25	chr22:30712400-30717200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr22:30712600-30718800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr22:30713600-30717800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr22:30713600-30717800	Enhancers	Pancreas	Pancrea
29	chr22:30713800-30717400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr22:30713800-30719800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr22:30713800-30721000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr22:30714000-30717000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr22:30714000-30718600	Enhancers	Right Atrium	heart
34	chr22:30714200-30717000	Strong transcription	HSMM	muscle
35	chr22:30714200-30717200	Genic enhancers	Lung	lung
36	chr22:30714200-30718000	Enhancers	Liver	Liver
37	chr22:30714200-30718000	Enhancers	Left Ventricle	heart
38	chr22:30714400-30717000	Genic enhancers	Duodenum Mucosa	Duodenum
39	chr22:30714400-30718600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr22:30714400-30719400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr22:30714600-30717000	Weak transcription	Aorta	Aorta
42	chr22:30714600-30717400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr22:30714600-30717600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr22:30714800-30717000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr22:30714800-30717000	Strong transcription	Fetal Muscle Leg	muscle
46	chr22:30714800-30717400	Strong transcription	Osteobl	bone
47	chr22:30715000-30717000	Genic enhancers	Adipose Nuclei	Adipose
48	chr22:30715000-30717200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr22:30715000-30717400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr22:30715000-30717600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links