Variant report

Variant	rs12169823
Chromosome Location	chr22:30390654-30390655
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30231401..30237558-chr22:30387473..30391733,6	MCF-7	breast:
2	chr22:30210116..30212715-chr22:30390306..30391990,2	MCF-7	breast:
3	chr22:30388182..30392809-chr22:30393222..30398050,6	K562	blood:
4	chr22:30388710..30391580-chr22:30397983..30401344,3	MCF-7	breast:
5	chr22:30388182..30391432-chr22:30393585..30396816,3	K562	blood:

Variant related genes	Relation type
ENSG00000100325	Chromatin interaction
ENSG00000100330	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10222281	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11090591	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11090592	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11090597	0.90[AMR][1000 genomes]
rs11704206	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11704885	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705048	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs11705207	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705418	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12159277	0.80[CHB][hapmap]
rs12165769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12166755	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12166998	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12169403	1.00[CEU][hapmap]
rs12330007	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12330076	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12627856	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12627866	0.80[CHB][hapmap]
rs12627944	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12628395	0.83[ASN][1000 genomes]
rs12628545	0.80[CHB][hapmap]
rs16988049	0.80[CHB][hapmap]
rs17644868	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17644886	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17647135	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17711461	0.80[CHB][hapmap]
rs17711508	0.80[CHB][hapmap]
rs17713646	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240366	0.80[CHB][hapmap]
rs28520101	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28635872	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34647160	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747148	0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3788418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3788425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285800	0.80[CHB][hapmap]
rs737905	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs739615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs740116	0.80[CHB][hapmap]
rs916782	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9614123	1.00[JPT][hapmap]
rs9620928	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9620929	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9620935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620944	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9620948	0.90[AMR][1000 genomes]
rs9625883	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9625886	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9625887	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9625889	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9625894	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625895	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625896	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625899	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9625910	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9625914	0.90[AMR][1000 genomes]
rs9625922	0.85[AMR][1000 genomes]
rs9625924	0.81[AMR][1000 genomes]
rs9625930	0.90[AMR][1000 genomes]

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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30350600-30402600	Weak transcription	Aorta	Aorta
2	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr22:30366600-30390800	Weak transcription	Gastric	stomach
4	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr22:30367400-30397800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr22:30370000-30391000	Weak transcription	Fetal Heart	heart
7	chr22:30370600-30390800	Weak transcription	Right Ventricle	heart
8	chr22:30373800-30391400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr22:30375200-30403200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr22:30375400-30390800	Weak transcription	Pancreas	Pancrea
11	chr22:30376200-30394800	Weak transcription	GM12878-XiMat	blood
12	chr22:30377600-30402800	Weak transcription	Fetal Brain Male	brain
13	chr22:30378200-30398800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr22:30378400-30391400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr22:30379200-30391200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr22:30379800-30390800	Weak transcription	Esophagus	oesophagus
17	chr22:30380800-30391800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr22:30381000-30397600	Weak transcription	Fetal Kidney	kidney
19	chr22:30382600-30392000	Strong transcription	Primary T cells from cord blood	blood
20	chr22:30383800-30391600	Strong transcription	Primary B cells from cord blood	blood
21	chr22:30384200-30391000	Weak transcription	Brain Substantia Nigra	brain
22	chr22:30384200-30398400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr22:30384200-30403800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr22:30384400-30393400	Weak transcription	Brain Hippocampus Middle	brain
25	chr22:30384400-30404000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr22:30384800-30390800	Strong transcription	Primary hematopoietic stem cells	blood
27	chr22:30385000-30404000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr22:30386200-30402600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr22:30386600-30390800	Strong transcription	Adipose Nuclei	Adipose
30	chr22:30386600-30391200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr22:30386800-30391000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr22:30387200-30390800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr22:30387400-30390800	Strong transcription	Fetal Muscle Leg	muscle
34	chr22:30387400-30391000	Strong transcription	Fetal Thymus	thymus
35	chr22:30387600-30391400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr22:30388000-30390800	Weak transcription	Brain Anterior Caudate	brain
37	chr22:30388000-30390800	Weak transcription	Fetal Intestine Large	intestine
38	chr22:30388000-30394400	Weak transcription	Lung	lung
39	chr22:30388000-30394600	Weak transcription	Fetal Lung	lung
40	chr22:30388000-30398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr22:30388200-30390800	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr22:30388200-30391800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr22:30388200-30392200	Enhancers	HMEC	breast
44	chr22:30388400-30391000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr22:30388400-30391800	Enhancers	NH-A	brain
46	chr22:30388400-30392200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr22:30388400-30392200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr22:30388600-30390800	Weak transcription	Ovary	ovary
49	chr22:30388600-30390800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr22:30388600-30396800	Weak transcription	Brain Germinal Matrix	brain

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