Variant report

Variant	rs55883820
Chromosome Location	chr22:32007863-32007864
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	chr22:32007576-32007920	GM12892	blood:	n/a	n/a
2	POLR2A	chr22:32007661-32008042	HepG2	liver:	n/a	n/a
3	POLR2A	chr22:32007427-32007991	GM12878	blood:	n/a	n/a
4	POLR2A	chr22:32007717-32007897	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:32000648..32004011-chr22:32006419..32009000,3	K562	blood:
2	chr22:32006220..32009486-chr22:32009995..32012615,3	K562	blood:

Variant related genes	Relation type
SFI1	TF binding region
ENSG00000198089	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16989291	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3747156	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3747157	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55989741	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56219558	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56338522	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5994404	0.89[EUR][1000 genomes]
rs5994405	0.89[EUR][1000 genomes]
rs5994412	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73160657	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73160662	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73160669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73160697	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8139890	0.95[EUR][1000 genomes];0.89[ASN][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	nsv914980	chr22:31966274-32024980	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv517534	chr22:31977594-32024980	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv829176	chr22:31998223-32029556	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31935800-32013200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr22:31947800-32009600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr22:31949400-32014400	Weak transcription	Hela-S3	cervix
4	chr22:31957400-32016400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:31976200-32014800	Weak transcription	A549	lung
6	chr22:31976400-32014800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr22:31976400-32019200	Weak transcription	Fetal Brain Male	brain
8	chr22:31985600-32014000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:31985800-32010400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr22:31985800-32012400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr22:31985800-32014400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr22:31985800-32014800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:31990400-32014200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr22:31993200-32013800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr22:31996000-32008400	Strong transcription	Primary T cells from cord blood	blood
16	chr22:31996200-32010000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr22:31996400-32010800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr22:31996600-32010600	Strong transcription	Thymus	Thymus
19	chr22:31996600-32011200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr22:31996600-32011800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr22:31996600-32012200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr22:31996600-32018200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr22:31996600-32020600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr22:31996800-32011600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr22:31997200-32012000	Strong transcription	Fetal Thymus	thymus
26	chr22:31997400-32010400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr22:31997600-32008000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr22:31997600-32011400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr22:31998000-32008000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr22:31998400-32008000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr22:31998400-32015600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr22:31998600-32022000	Weak transcription	Fetal Kidney	kidney
33	chr22:31998800-32010200	Weak transcription	Left Ventricle	heart
34	chr22:31998800-32012200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr22:31999000-32010000	Weak transcription	Right Ventricle	heart
36	chr22:31999000-32010200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr22:31999000-32010600	Weak transcription	Osteobl	bone
38	chr22:31999000-32011800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr22:31999000-32013800	Weak transcription	HMEC	breast
40	chr22:31999000-32014600	Weak transcription	NHDF-Ad	bronchial
41	chr22:31999200-32010600	Weak transcription	HUVEC	blood vessel
42	chr22:31999400-32008400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr22:31999400-32011400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr22:31999400-32011600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr22:31999400-32012800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr22:31999400-32014800	Weak transcription	NH-A	brain
47	chr22:31999600-32012200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr22:31999800-32012200	Weak transcription	Brain Substantia Nigra	brain
49	chr22:32000200-32014600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr22:32001200-32012000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links