Variant report

Variant	rs2629451
Chromosome Location	chr12:56590550-56590551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56582670..56585645-chr12:56588160..56590728,3	MCF-7	breast:
2	chr12:56509396..56513116-chr12:56590002..56592493,3	K562	blood:
3	chr12:56587021..56588859-chr12:56589335..56591396,2	MCF-7	breast:
4	chr12:56579404..56590957-chr12:56614094..56620955,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139579	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000229117	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10747763	0.95[ASN][1000 genomes]
rs10876878	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11171772	1.00[ASN][1000 genomes]
rs11171777	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11834728	0.83[ASN][1000 genomes]
rs12229022	0.95[ASN][1000 genomes]
rs12320265	1.00[ASN][1000 genomes]
rs1274502	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1274503	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1405859	1.00[ASN][1000 genomes]
rs17118333	0.83[ASN][1000 genomes]
rs2271188	0.83[ASN][1000 genomes]
rs2271190	0.83[ASN][1000 genomes]
rs2463365	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2629453	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2695783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2695784	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28676339	0.83[ASN][1000 genomes]
rs2930787	0.95[AMR][1000 genomes]
rs2930788	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2950573	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3759096	0.83[ASN][1000 genomes]
rs3802996	0.83[ASN][1000 genomes]
rs3809130	0.83[ASN][1000 genomes]
rs4759218	0.95[ASN][1000 genomes]
rs56851901	0.83[ASN][1000 genomes]
rs57280585	0.83[ASN][1000 genomes]
rs57822276	0.83[ASN][1000 genomes]
rs58009483	1.00[ASN][1000 genomes]
rs58476735	0.83[ASN][1000 genomes]
rs58548156	0.83[ASN][1000 genomes]
rs58663297	0.83[ASN][1000 genomes]
rs59053322	1.00[ASN][1000 genomes]
rs59078852	1.00[ASN][1000 genomes]
rs59966703	1.00[ASN][1000 genomes]
rs60396934	0.83[ASN][1000 genomes]
rs61939011	1.00[ASN][1000 genomes]
rs6581091	0.95[ASN][1000 genomes]
rs703823	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7311008	0.95[ASN][1000 genomes]
rs7489249	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs773654	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs773655	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs773658	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs773659	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs773660	0.90[ASN][1000 genomes]
rs773661	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7956599	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7956926	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7962107	1.00[ASN][1000 genomes]
rs7967464	1.00[ASN][1000 genomes]
rs7975405	1.00[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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv973989	chr12:56582243-56602996	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56584200-56598000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:56584600-56598000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:56584600-56598000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:56584600-56598200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:56584600-56598400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:56584600-56600000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:56584800-56590800	Weak transcription	Fetal Heart	heart
8	chr12:56584800-56591400	Weak transcription	NHLF	lung
9	chr12:56584800-56596400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:56584800-56597800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:56584800-56597800	Weak transcription	Fetal Thymus	thymus
12	chr12:56584800-56598000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:56584800-56598000	Weak transcription	Primary B cells from cord blood	blood
14	chr12:56584800-56598000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:56584800-56598000	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:56584800-56598000	Weak transcription	Fetal Stomach	stomach
17	chr12:56584800-56598200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:56584800-56598400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:56584800-56598600	Weak transcription	Ovary	ovary
20	chr12:56584800-56598800	Weak transcription	HMEC	breast
21	chr12:56584800-56599000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:56584800-56599400	Weak transcription	Pancreas	Pancrea
23	chr12:56584800-56599600	Weak transcription	Colonic Mucosa	Colon
24	chr12:56585000-56590600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:56585000-56592000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:56585000-56592600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:56585000-56592600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:56585000-56597800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr12:56585000-56597800	Weak transcription	Primary T cells from cord blood	blood
30	chr12:56585000-56597800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr12:56585000-56598000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr12:56585000-56598000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:56585000-56598000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:56585000-56598000	Weak transcription	Fetal Brain Female	brain
35	chr12:56585000-56598000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:56585000-56598200	Weak transcription	A549	lung
37	chr12:56585000-56598400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:56585000-56598400	Weak transcription	NHDF-Ad	bronchial
39	chr12:56585000-56614800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr12:56585200-56590800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:56585200-56592800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr12:56585200-56598000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:56585400-56590600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:56585800-56590600	Weak transcription	Adipose Nuclei	Adipose
45	chr12:56585800-56598200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:56587200-56590600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:56587200-56598000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:56587200-56598000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:56587200-56598200	Weak transcription	Brain Substantia Nigra	brain
50	chr12:56587200-56598600	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links