Variant report

Variant	rs12628545
Chromosome Location	chr22:30205937-30205938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30203989..30206698-chr22:30207811..30209768,4	MCF-7	breast:
2	chr22:30161016..30163060-chr22:30205322..30207910,2	MCF-7	breast:
3	chr22:30199847..30201842-chr22:30205900..30208227,2	MCF-7	breast:
4	chr22:30203954..30206021-chr22:30210250..30212247,2	MCF-7	breast:
5	chr22:30205102..30207625-chr22:30210050..30212988,2	MCF-7	breast:
6	chr22:30193309..30197041-chr22:30202385..30207780,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100325	Chromatin interaction
ENSG00000100319	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10483156	0.80[CHB][hapmap]
rs1071962	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12158466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12159277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12165769	0.80[CHB][hapmap]
rs12166087	0.80[CHB][hapmap]
rs12169823	0.80[CHB][hapmap]
rs12627866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12628028	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12628234	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12628294	0.81[ASN][1000 genomes]
rs14115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16987142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16988049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17711461	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17711508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018808	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240364	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs249399	1.00[ASN][1000 genomes]
rs249402	0.92[ASN][1000 genomes]
rs28730892	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788418	0.80[CHB][hapmap]
rs3788425	0.80[CHB][hapmap]
rs57122143	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58015017	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59394320	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5997515	1.00[CEU][hapmap]
rs5997518	0.87[EUR][1000 genomes]
rs5997519	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5997520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5997524	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6006234	1.00[CEU][hapmap]
rs6006235	1.00[CEU][hapmap]
rs6006238	1.00[CEU][hapmap]
rs6006239	1.00[CEU][hapmap]
rs6006241	0.87[EUR][1000 genomes]
rs6006242	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6006247	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6006249	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6006250	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6006262	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60805530	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61616383	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61736786	0.81[ASN][1000 genomes]
rs7285660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7287777	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7289250	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7290420	1.00[CEU][hapmap]
rs73392899	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73394814	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394831	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394838	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737721	0.88[ASN][1000 genomes]
rs737728	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs737906	0.80[CHB][hapmap]
rs737907	0.80[CHB][hapmap]
rs740116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8138165	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9620935	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30182200-30217000	Strong transcription	Fetal Intestine Small	intestine
3	chr22:30182200-30222200	Strong transcription	Thymus	Thymus
4	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
5	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
6	chr22:30183000-30221400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr22:30183400-30224000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr22:30183800-30224000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr22:30184000-30222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:30191000-30222200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr22:30193400-30217200	Strong transcription	Fetal Thymus	thymus
15	chr22:30194200-30212200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr22:30195400-30222000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr22:30195400-30222200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr22:30195600-30208200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr22:30196000-30212000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr22:30196000-30217000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr22:30196200-30207000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr22:30196200-30211800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr22:30196200-30215400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr22:30196200-30217200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr22:30196200-30217200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr22:30196200-30222200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr22:30196200-30222200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr22:30196400-30211800	Strong transcription	Placenta	Placenta
29	chr22:30196400-30221200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:30197000-30206200	Strong transcription	Liver	Liver
31	chr22:30197000-30222200	Strong transcription	Dnd41	blood
32	chr22:30197400-30216000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr22:30197400-30216200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr22:30197800-30206000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr22:30198000-30211800	Strong transcription	Left Ventricle	heart
36	chr22:30198200-30211800	Weak transcription	Right Atrium	heart
37	chr22:30198400-30207200	Weak transcription	Hela-S3	cervix
38	chr22:30199200-30211800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr22:30199200-30222000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr22:30199400-30211000	Strong transcription	Right Ventricle	heart
41	chr22:30199400-30211800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr22:30200600-30211400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr22:30202400-30206000	Weak transcription	Fetal Brain Male	brain
44	chr22:30202400-30207400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr22:30202400-30208200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr22:30202800-30206000	Weak transcription	NHDF-Ad	bronchial
47	chr22:30202800-30207000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr22:30202800-30207400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr22:30203000-30206000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr22:30203000-30206000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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