Variant report

Variant	rs1904242
Chromosome Location	chr12:12132490-12132491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10743973	0.93[ASN][1000 genomes]
rs12315516	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12316914	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1871286	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1904239	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1904241	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763743	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4763744	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4763748	0.83[EUR][1000 genomes]
rs4763749	0.83[EUR][1000 genomes]
rs6488475	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488476	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488482	0.82[EUR][1000 genomes]
rs6488483	0.82[EUR][1000 genomes]
rs7303792	0.82[EUR][1000 genomes]
rs7312970	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7954303	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7956839	0.93[ASN][1000 genomes]
rs7958862	0.83[EUR][1000 genomes]
rs7962986	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7965081	0.82[EUR][1000 genomes]
rs7968948	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7968953	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7976590	0.93[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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898804	chr12:12058411-12202173	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv898805	chr12:12119414-12156322	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv19512	chr12:12130988-12147206	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12128800-12134400	Weak transcription	Right Atrium	heart
2	chr12:12129600-12132600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:12129600-12132800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:12129800-12132800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:12130400-12137400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:12131000-12132800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:12131000-12135600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr12:12131000-12135600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr12:12131600-12132600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:12131600-12132600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:12131600-12133000	Enhancers	GM12878-XiMat	blood
12	chr12:12131600-12133000	Enhancers	HMEC	breast
13	chr12:12131600-12133200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:12131600-12134200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr12:12131600-12134400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:12131600-12135400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:12131600-12135400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:12131600-12135600	Enhancers	Primary T cells fromperipheralblood	blood
19	chr12:12131800-12132800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:12131800-12134400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:12132000-12133200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr12:12132200-12132600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:12132200-12132800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr12:12132200-12134000	Weak transcription	HSMM	muscle
25	chr12:12132200-12134200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:12132200-12139200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:12132400-12134000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:12132400-12134000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:12132400-12134000	Weak transcription	NHEK	skin
30	chr12:12132400-12134000	Weak transcription	Osteobl	bone
31	chr12:12132400-12134200	Weak transcription	NH-A	brain
32	chr12:12132400-12135400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links