Variant report

Variant	rs5762474
Chromosome Location	chr22:28488295-28488296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28487019..28489734-chr22:28491482..28493153,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11912165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2064360	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2294969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28720063	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56695231	0.97[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs5752658	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5752679	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[LWK][hapmap];0.85[AFR][1000 genomes]
rs5752687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs5752690	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5752693	0.96[EUR][1000 genomes]
rs5762408	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5762446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs5762449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs5762478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762492	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5762495	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5762504	0.82[ASN][1000 genomes]
rs5762506	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs5762540	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28466400-28489800	Weak transcription	Fetal Brain Male	brain
2	chr22:28466600-28503600	Weak transcription	Hela-S3	cervix
3	chr22:28468600-28489800	Weak transcription	Fetal Kidney	kidney
4	chr22:28471600-28491800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr22:28471800-28488400	Weak transcription	Left Ventricle	heart
6	chr22:28471800-28491400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr22:28471800-28492000	Weak transcription	Aorta	Aorta
8	chr22:28472000-28489600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr22:28472000-28489800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr22:28472000-28494800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr22:28472000-28499000	Weak transcription	NHDF-Ad	bronchial
12	chr22:28472200-28498600	Weak transcription	Colon Smooth Muscle	Colon
13	chr22:28472400-28494200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr22:28472800-28495400	Weak transcription	Pancreas	Pancrea
15	chr22:28472800-28501000	Weak transcription	Gastric	stomach
16	chr22:28474000-28488600	Weak transcription	Fetal Lung	lung
17	chr22:28475200-28489800	Weak transcription	Fetal Heart	heart
18	chr22:28480200-28493600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr22:28480400-28490000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr22:28480400-28490000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr22:28480400-28490000	Weak transcription	Brain Germinal Matrix	brain
22	chr22:28480400-28492000	Weak transcription	Fetal Intestine Small	intestine
23	chr22:28480400-28494000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr22:28483600-28500000	Weak transcription	Spleen	Spleen
25	chr22:28485600-28494200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr22:28485600-28494600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr22:28485800-28501400	Strong transcription	Dnd41	blood
28	chr22:28485800-28508600	Weak transcription	Brain Substantia Nigra	brain
29	chr22:28486000-28492200	Weak transcription	Lung	lung
30	chr22:28486000-28507200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr22:28486200-28489600	Weak transcription	Primary T cells from cord blood	blood
32	chr22:28486200-28504400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr22:28486200-28504800	Weak transcription	Osteobl	bone
34	chr22:28486400-28490000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr22:28486400-28494000	Weak transcription	Right Ventricle	heart
36	chr22:28486400-28508600	Weak transcription	Psoas Muscle	Psoas
37	chr22:28486600-28498400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr22:28486600-28499400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr22:28486600-28499400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr22:28486800-28489000	Strong transcription	Fetal Brain Female	brain
41	chr22:28486800-28489600	Weak transcription	HepG2	liver
42	chr22:28486800-28490000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr22:28486800-28490000	Strong transcription	Fetal Muscle Leg	muscle
44	chr22:28486800-28491200	Strong transcription	Adipose Nuclei	Adipose
45	chr22:28486800-28494800	Weak transcription	Brain Angular Gyrus	brain
46	chr22:28486800-28498600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr22:28487000-28490200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr22:28487000-28496800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr22:28487400-28488600	Strong transcription	Fetal Stomach	stomach
50	chr22:28487400-28488600	Strong transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links