Variant report

Variant	rs60254089
Chromosome Location	chr12:123740328-123740329
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	chr12:123738852..123742382-chr12:123742428..123743998,3	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10732573	0.95[ASN][1000 genomes]
rs10734901	0.95[ASN][1000 genomes]
rs10744150	0.81[ASN][1000 genomes]
rs10744151	0.84[ASN][1000 genomes]
rs10772997	0.84[ASN][1000 genomes]
rs10772999	0.88[ASN][1000 genomes]
rs10773002	0.90[ASN][1000 genomes]
rs11057202	0.84[ASN][1000 genomes]
rs11057205	0.88[ASN][1000 genomes]
rs11057207	0.88[ASN][1000 genomes]
rs11057209	0.89[ASN][1000 genomes]
rs11554169	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1568427	0.92[ASN][1000 genomes]
rs1609520	0.94[ASN][1000 genomes]
rs1727331	0.83[ASN][1000 genomes]
rs1969355	0.97[ASN][1000 genomes]
rs1980251	0.95[ASN][1000 genomes]
rs2090764	0.93[ASN][1000 genomes]
rs2280424	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3759114	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4474478	0.89[ASN][1000 genomes]
rs4474479	0.89[ASN][1000 genomes]
rs4594040	0.89[ASN][1000 genomes]
rs4759372	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4759411	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4759413	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4759414	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4759418	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61231969	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61519741	0.88[ASN][1000 genomes]
rs7137286	0.88[ASN][1000 genomes]
rs7304782	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:123733400-123745000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:123735000-123740400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:123735200-123751800	Strong transcription	Fetal Stomach	stomach
6	chr12:123735400-123745400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:123735600-123743400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:123735600-123752400	Strong transcription	Thymus	Thymus
9	chr12:123736000-123740600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:123736000-123745400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:123736000-123747800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:123736000-123748000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:123736000-123752200	Strong transcription	Dnd41	blood
14	chr12:123736200-123742400	Strong transcription	Fetal Thymus	thymus
15	chr12:123736200-123744200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:123736200-123751400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:123736400-123750600	Strong transcription	Fetal Lung	lung
18	chr12:123736400-123752200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:123736400-123752600	Strong transcription	NHLF	lung
20	chr12:123736600-123740400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:123737000-123744000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:123737000-123753000	Strong transcription	Fetal Intestine Small	intestine
23	chr12:123737200-123752000	Strong transcription	A549	lung
24	chr12:123737400-123749000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:123737800-123741400	Strong transcription	Colonic Mucosa	Colon
26	chr12:123737800-123742000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:123737800-123743800	Strong transcription	GM12878-XiMat	blood
28	chr12:123737800-123745000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:123737800-123745600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:123737800-123746800	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:123738000-123741000	Strong transcription	Primary B cells from cord blood	blood
32	chr12:123738000-123742600	Strong transcription	HepG2	liver
33	chr12:123738000-123743400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr12:123738000-123743400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:123738000-123743600	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:123738000-123743600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:123738000-123743800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:123738000-123743800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:123738000-123744000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:123738000-123744600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:123738000-123745200	Strong transcription	Spleen	Spleen
42	chr12:123738000-123746000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr12:123738000-123746200	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr12:123738000-123746200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:123738000-123746600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:123738000-123748200	Strong transcription	Primary T cells from cord blood	blood
47	chr12:123738000-123749200	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr12:123738000-123749200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:123738000-123749600	Strong transcription	Fetal Muscle Leg	muscle
50	chr12:123738000-123749600	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links