Variant report

Variant	rs11171774
Chromosome Location	chr12:56589227-56589228
allele	A/C
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	chr12:56586857..56589581-chr12:56659506..56661995,3	K562	blood:
3	chr12:56583715..56585705-chr12:56588416..56589988,2	K562	blood:
4	chr12:56579404..56590957-chr12:56614094..56620955,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139613	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000258199	Chromatin interaction

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

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

rs_ID	r²[population]
rs10747762	0.91[AMR][1000 genomes]
rs1274501	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1995742	1.00[AMR][1000 genomes]
rs2066811	0.90[AMR][1000 genomes]
rs2450101	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2450104	1.00[AMR][1000 genomes]
rs2629449	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4759219	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7301099	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773644	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs773647	0.93[AFR][1000 genomes];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	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:67 , 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	chr12:56584800-56590000	Weak transcription	Placenta	Placenta
8	chr12:56584800-56590200	Weak transcription	NH-A	brain
9	chr12:56584800-56590800	Weak transcription	Fetal Heart	heart
10	chr12:56584800-56591400	Weak transcription	NHLF	lung
11	chr12:56584800-56596400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:56584800-56597800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:56584800-56597800	Weak transcription	Fetal Thymus	thymus
14	chr12:56584800-56598000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:56584800-56598000	Weak transcription	Primary B cells from cord blood	blood
16	chr12:56584800-56598000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:56584800-56598000	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:56584800-56598000	Weak transcription	Fetal Stomach	stomach
19	chr12:56584800-56598200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:56584800-56598400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr12:56584800-56598600	Weak transcription	Ovary	ovary
22	chr12:56584800-56598800	Weak transcription	HMEC	breast
23	chr12:56584800-56599000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:56584800-56599400	Weak transcription	Pancreas	Pancrea
25	chr12:56584800-56599600	Weak transcription	Colonic Mucosa	Colon
26	chr12:56585000-56590600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:56585000-56592000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:56585000-56592600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:56585000-56592600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:56585000-56597800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr12:56585000-56597800	Weak transcription	Primary T cells from cord blood	blood
32	chr12:56585000-56597800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:56585000-56598000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:56585000-56598000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:56585000-56598000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:56585000-56598000	Weak transcription	Fetal Brain Female	brain
37	chr12:56585000-56598000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:56585000-56598200	Weak transcription	A549	lung
39	chr12:56585000-56598400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr12:56585000-56598400	Weak transcription	NHDF-Ad	bronchial
41	chr12:56585000-56614800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr12:56585200-56590800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:56585200-56592800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:56585200-56598000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:56585400-56590600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:56585800-56590600	Weak transcription	Adipose Nuclei	Adipose
47	chr12:56585800-56598200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr12:56587200-56590000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:56587200-56590600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:56587200-56598000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links