Variant report

Variant	rs2657877
Chromosome Location	chr12:56881352-56881353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56862344..56864045-chr12:56880136..56881879,2	MCF-7	breast:
2	chr12:56726722..56729321-chr12:56880761..56882422,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135517	Chromatin interaction
ENSG00000135473	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10747768	1.00[MEX][hapmap]
rs10876892	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2638298	1.00[MEX][hapmap]
rs2638317	0.84[ASW][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2638336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2657887	0.83[ASW][hapmap];1.00[MEX][hapmap]
rs2933240	0.83[AMR][1000 genomes]
rs2939307	0.80[AMR][1000 genomes]
rs3809122	0.83[YRI][hapmap]
rs774212	1.00[AMR][1000 genomes]
rs812282	1.00[AMR][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	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
2	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
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv3326032	chr12:56881235-56884033	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56863400-56881400	Weak transcription	HSMMtube	muscle
2	chr12:56863800-56881600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:56865600-56881400	Weak transcription	Aorta	Aorta
4	chr12:56867600-56881800	Weak transcription	A549	lung
5	chr12:56869000-56881600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:56879800-56882600	Flanking Active TSS	Liver	Liver
7	chr12:56880800-56881400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
8	chr12:56880800-56881400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
9	chr12:56880800-56881400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
10	chr12:56880800-56881400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr12:56880800-56881400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr12:56880800-56881400	Active TSS	Pancreas	Pancrea
13	chr12:56880800-56881400	Enhancers	Spleen	Spleen
14	chr12:56880800-56881400	Flanking Active TSS	HepG2	liver
15	chr12:56880800-56881600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:56880800-56881600	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr12:56880800-56882600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr12:56880800-56882600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr12:56880800-56882800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr12:56880800-56882800	Active TSS	Brain Angular Gyrus	brain
21	chr12:56880800-56882800	Active TSS	Brain Substantia Nigra	brain
22	chr12:56881000-56881400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
23	chr12:56881000-56881400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:56881000-56881400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr12:56881000-56881400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:56881000-56881400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr12:56881000-56881400	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr12:56881000-56881400	Bivalent Enhancer	Fetal Stomach	stomach
29	chr12:56881000-56881400	Bivalent Enhancer	Fetal Thymus	thymus
30	chr12:56881000-56881400	ZNF genes & repeats	HSMM	muscle
31	chr12:56881000-56882000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:56881000-56882200	Bivalent/Poised TSS	Fetal Brain Female	brain
33	chr12:56881000-56882600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr12:56881000-56882600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:56881000-56882600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
36	chr12:56881000-56882600	Flanking Active TSS	HMEC	breast
37	chr12:56881000-56882800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr12:56881200-56881400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:56881200-56881400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:56881200-56881400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:56881200-56881400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:56881200-56881400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
43	chr12:56881200-56881400	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:56881200-56881400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:56881200-56881400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
46	chr12:56881200-56881400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr12:56881200-56881400	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr12:56881200-56881400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
49	chr12:56881200-56881400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:56881200-56881400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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