Variant report

Variant	rs12628239
Chromosome Location	chr22:29096361-29096362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29094612..29096688-chr22:29136318..29138280,2	K562	blood:

Variant related genes	Relation type
ENSG00000183765	Chromatin interaction
ENSG00000100209	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1547014	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1972202	0.82[AMR][1000 genomes]
rs2078555	0.86[EUR][1000 genomes]
rs4490290	0.83[AMR][1000 genomes]
rs4820791	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4822983	0.86[EUR][1000 genomes]
rs5752773	0.86[EUR][1000 genomes]
rs5752774	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5752775	0.86[EUR][1000 genomes]
rs5752776	0.86[EUR][1000 genomes]
rs5762752	0.84[AMR][1000 genomes]
rs5762753	0.83[AMR][1000 genomes]
rs6005837	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6005840	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs743184	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv459867	chr22:28993183-29109036	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv588881	chr22:28993183-29109036	Weak transcription Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1064624	chr22:29065528-29130728	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	esv17527	chr22:29066121-29102976	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv513775	chr22:29083731-29137822	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29076200-29103000	Weak transcription	GM12878-XiMat	blood
2	chr22:29076200-29137600	Weak transcription	Esophagus	oesophagus
3	chr22:29076400-29098000	Weak transcription	Ovary	ovary
4	chr22:29076400-29099400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr22:29076400-29102000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:29076400-29103000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr22:29076400-29105000	Weak transcription	HUVEC	blood vessel
8	chr22:29076400-29105200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr22:29076400-29105800	Weak transcription	NHLF	lung
10	chr22:29076400-29119200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr22:29076400-29129400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr22:29076600-29102200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr22:29077200-29105000	Weak transcription	Osteobl	bone
14	chr22:29077400-29102000	Weak transcription	Fetal Intestine Large	intestine
15	chr22:29077400-29106000	Weak transcription	A549	lung
16	chr22:29077600-29099000	Weak transcription	Hela-S3	cervix
17	chr22:29077600-29102800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr22:29079600-29130200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr22:29082200-29109800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr22:29082800-29106000	Weak transcription	Liver	Liver
21	chr22:29082800-29137600	Weak transcription	Spleen	Spleen
22	chr22:29083000-29126600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr22:29083600-29104000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr22:29084200-29099000	Weak transcription	Fetal Thymus	thymus
25	chr22:29084600-29097800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr22:29085000-29116600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr22:29085800-29102200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr22:29085800-29105000	Weak transcription	HMEC	breast
29	chr22:29086200-29106600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr22:29086400-29106000	Weak transcription	HSMM	muscle
31	chr22:29087800-29106200	Weak transcription	Fetal Lung	lung
32	chr22:29088600-29118600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr22:29089600-29100400	Weak transcription	Lung	lung
34	chr22:29090200-29129000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr22:29090400-29097400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr22:29090400-29099400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr22:29090400-29100800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr22:29090400-29106000	Weak transcription	HSMMtube	muscle
39	chr22:29090400-29110800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr22:29090600-29137200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr22:29090600-29137200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr22:29090800-29099000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr22:29090800-29108000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr22:29091000-29104000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr22:29091000-29116600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr22:29091000-29120200	Weak transcription	Placenta	Placenta
47	chr22:29091200-29098800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr22:29092000-29100400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr22:29092000-29108600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr22:29092400-29096800	Strong transcription	Fetal Intestine Small	intestine

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