Variant report

Variant	rs138648
Chromosome Location	chr22:28391157-28391158
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	chr22:28391135-28391196	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr22:28390570-28391422	K562	blood:	n/a	n/a
3	POLR2A	chr22:28391111-28391295	HepG2	liver:	n/a	n/a
4	POLR2A	chr22:28391125-28391301	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28387405..28389960-chr22:28390673..28392531,2	K562	blood:

Variant related genes	Relation type
TTC28-AS1	TF binding region
ENSG00000235954	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10154425	0.89[CEU][hapmap]
rs12166077	0.89[CEU][hapmap]
rs12167128	0.82[ASW][hapmap];0.90[MEX][hapmap]
rs12168054	0.89[CEU][hapmap]
rs12170161	0.80[MEX][hapmap]
rs12170953	0.89[CEU][hapmap]
rs130414	0.90[MEX][hapmap]
rs135648	0.80[MEX][hapmap]
rs138645	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs138646	1.00[ASW][hapmap];0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs138651	0.86[CEU][hapmap]
rs138653	0.89[CEU][hapmap]
rs138654	0.89[CEU][hapmap]
rs138656	0.89[CEU][hapmap]
rs138658	0.89[CEU][hapmap]
rs138660	0.89[CEU][hapmap]
rs138664	0.89[CEU][hapmap]
rs138665	0.89[CEU][hapmap]
rs138667	0.89[CEU][hapmap]
rs138671	0.89[CEU][hapmap]
rs138676	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs138679	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs138680	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16985818	0.84[ASN][1000 genomes]
rs17407024	0.88[CEU][hapmap]
rs17483887	0.89[CEU][hapmap]
rs17484337	0.89[CEU][hapmap]
rs2143420	0.90[MEX][hapmap]
rs2745562	0.86[CEU][hapmap]
rs470101	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs470102	0.89[CEU][hapmap]
rs470103	0.89[CEU][hapmap]
rs73880371	0.82[EUR][1000 genomes]
rs9620762	0.89[CEU][hapmap]
rs9620764	0.89[CEU][hapmap]
rs9625387	0.89[CEU][hapmap]
rs9625390	0.89[CEU][hapmap]
rs9625391	0.89[CEU][hapmap]
rs9625408	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv522306	chr22:28378472-28402624	Strong transcription Enhancers Weak 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	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28360800-28392400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr22:28369200-28398400	Weak transcription	Hela-S3	cervix
3	chr22:28369400-28394000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr22:28371800-28395000	Weak transcription	Small Intestine	intestine
5	chr22:28373600-28404000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:28373800-28398200	Strong transcription	Fetal Brain Female	brain
7	chr22:28373800-28404200	Strong transcription	Fetal Stomach	stomach
8	chr22:28373800-28405200	Strong transcription	Fetal Intestine Small	intestine
9	chr22:28377800-28391800	Strong transcription	Fetal Lung	lung
10	chr22:28377800-28398000	Strong transcription	Fetal Intestine Large	intestine
11	chr22:28377800-28398600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr22:28378000-28396600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr22:28379400-28399600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr22:28381600-28393800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr22:28381800-28412400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr22:28382200-28394000	Weak transcription	Brain Substantia Nigra	brain
17	chr22:28382800-28391800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr22:28382800-28394600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr22:28384000-28405000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr22:28384200-28399400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr22:28384400-28392600	Strong transcription	Brain Germinal Matrix	brain
22	chr22:28384600-28397600	Strong transcription	Ovary	ovary
23	chr22:28384800-28401600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr22:28385000-28393400	Weak transcription	HSMM	muscle
25	chr22:28386200-28405800	Strong transcription	Dnd41	blood
26	chr22:28386200-28416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr22:28387400-28392400	Weak transcription	Osteobl	bone
28	chr22:28387400-28405200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr22:28387600-28393800	Weak transcription	NHDF-Ad	bronchial
30	chr22:28387600-28394600	Weak transcription	HepG2	liver
31	chr22:28387600-28398200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr22:28387600-28405000	Weak transcription	Fetal Kidney	kidney
33	chr22:28387800-28392000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr22:28387800-28392000	Strong transcription	Brain Anterior Caudate	brain
35	chr22:28387800-28392400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr22:28387800-28392400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr22:28387800-28395600	Strong transcription	Pancreas	Pancrea
38	chr22:28387800-28397400	Strong transcription	Placenta	Placenta
39	chr22:28387800-28399000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr22:28387800-28399200	Strong transcription	Fetal Muscle Leg	muscle
41	chr22:28388000-28393400	Strong transcription	Adipose Nuclei	Adipose
42	chr22:28388000-28397200	Strong transcription	Lung	lung
43	chr22:28388200-28392400	Strong transcription	Right Ventricle	heart
44	chr22:28388200-28392600	Strong transcription	Brain Cingulate Gyrus	brain
45	chr22:28388200-28396800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr22:28388400-28392200	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr22:28388400-28392400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr22:28388400-28393000	Weak transcription	Fetal Thymus	thymus
49	chr22:28388400-28393600	Weak transcription	Primary T cells from cord blood	blood
50	chr22:28388400-28393600	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links