Variant report

Variant	rs16986280
Chromosome Location	chr22:28695642-28695643
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	POLR2A	chr22:28695249-28695752	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr22:28695287-28695701	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
ENSG00000199797	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12484116	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs12484855	1.00[AFR][1000 genomes]
rs134190	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs134195	0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs135646	0.91[CHB][hapmap]
rs135654	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs16986431	0.84[JPT][hapmap]
rs16986442	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs16987010	1.00[CHB][hapmap]
rs5762543	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28679400-28695800	Weak transcription	Aorta	Aorta
2	chr22:28680200-28696000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr22:28680200-28696000	Weak transcription	NHDF-Ad	bronchial
4	chr22:28680200-28702000	Weak transcription	Osteobl	bone
5	chr22:28683400-28698200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr22:28685000-28704400	Weak transcription	Fetal Intestine Small	intestine
7	chr22:28690000-28702200	Weak transcription	Fetal Intestine Large	intestine
8	chr22:28690600-28695800	Strong transcription	Dnd41	blood
9	chr22:28692200-28698000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr22:28693000-28696800	Enhancers	Brain Hippocampus Middle	brain
11	chr22:28693200-28705600	Weak transcription	HepG2	liver
12	chr22:28693800-28702200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:28693800-28704000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr22:28693800-28709200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr22:28693800-28710400	Weak transcription	Fetal Stomach	stomach
16	chr22:28693800-28716000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr22:28694000-28705000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr22:28694200-28696000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr22:28694200-28696000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr22:28694200-28696000	Weak transcription	Liver	Liver
21	chr22:28694200-28696200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr22:28694200-28697000	Enhancers	Brain Substantia Nigra	brain
23	chr22:28694400-28704200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr22:28694600-28695800	Weak transcription	Brain Angular Gyrus	brain
25	chr22:28694600-28695800	Weak transcription	Right Atrium	heart
26	chr22:28694600-28711800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr22:28694800-28695800	Weak transcription	Gastric	stomach
28	chr22:28694800-28699000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr22:28695000-28696000	Enhancers	Fetal Brain Female	brain
30	chr22:28695000-28696200	Enhancers	Brain Anterior Caudate	brain
31	chr22:28695000-28696400	Enhancers	Colon Smooth Muscle	Colon
32	chr22:28695200-28696200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr22:28695200-28696200	Enhancers	Fetal Lung	lung
34	chr22:28695400-28695800	Enhancers	Stomach Smooth Muscle	stomach
35	chr22:28695400-28696000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr22:28695400-28696200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr22:28695400-28696200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr22:28695400-28696200	Enhancers	Left Ventricle	heart
39	chr22:28695400-28696200	Enhancers	Ovary	ovary
40	chr22:28695400-28696200	Enhancers	Pancreas	Pancrea
41	chr22:28695400-28696200	Enhancers	Rectal Smooth Muscle	rectum
42	chr22:28695400-28696200	Enhancers	Right Ventricle	heart
43	chr22:28695400-28696200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr22:28695400-28696400	Enhancers	Adipose Nuclei	Adipose
45	chr22:28695400-28696400	Enhancers	Brain Cingulate Gyrus	brain
46	chr22:28695400-28696400	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr22:28695400-28696800	Enhancers	Fetal Heart	heart
48	chr22:28695600-28695800	Enhancers	Small Intestine	intestine
49	chr22:28695600-28696000	Weak transcription	Fetal Muscle Leg	muscle
50	chr22:28695600-28702800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links