Variant report

Variant	rs73408887
Chromosome Location	chr12:123452184-123452185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123318760..123321217-chr12:123449684..123452450,2	K562	blood:
2	chr12:123449701..123452611-chr12:123716445..123719411,3	K562	blood:
3	chr12:123319262..123321924-chr12:123450152..123453465,3	K562	blood:
4	chr12:123355640..123358495-chr12:123449218..123452212,2	MCF-7	breast:
5	chr12:123428831..123432471-chr12:123448558..123452277,3	K562	blood:
6	chr12:123449477..123453379-chr12:123715163..123718004,4	MCF-7	breast:
7	chr12:123436728..123438817-chr12:123451024..123452828,2	MCF-7	breast:
8	chr12:123449332..123452871-chr12:123717386..123719515,4	K562	blood:
9	chr12:122983924..122985565-chr12:123450706..123452240,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000051825	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000033030	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs34010146	0.85[AMR][1000 genomes]
rs55646110	0.85[AMR][1000 genomes]
rs55796417	1.00[AMR][1000 genomes]
rs55813219	0.85[AMR][1000 genomes]
rs55830208	1.00[AMR][1000 genomes]
rs55939945	0.85[AMR][1000 genomes]
rs55951195	0.85[AMR][1000 genomes]
rs56000615	0.85[AMR][1000 genomes]
rs56020503	1.00[AMR][1000 genomes]
rs56150478	1.00[AMR][1000 genomes]
rs56288804	1.00[AMR][1000 genomes]
rs56725866	1.00[AMR][1000 genomes]
rs57110420	0.85[AMR][1000 genomes]
rs57258703	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57863319	1.00[AMR][1000 genomes]
rs58025094	0.85[AMR][1000 genomes]
rs58462666	0.85[AMR][1000 genomes]
rs59081274	0.85[AMR][1000 genomes]
rs59211448	1.00[AMR][1000 genomes]
rs59379557	1.00[AMR][1000 genomes]
rs59526938	0.85[AMR][1000 genomes]
rs60341839	1.00[AMR][1000 genomes]
rs60739634	0.85[AMR][1000 genomes]
rs60809882	1.00[AMR][1000 genomes]
rs60888713	0.85[AMR][1000 genomes]
rs60901287	0.85[AMR][1000 genomes]
rs60920158	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60987910	1.00[AMR][1000 genomes]
rs61061591	0.85[AMR][1000 genomes]
rs61377358	1.00[AMR][1000 genomes]
rs61516893	1.00[AMR][1000 genomes]
rs61546241	0.85[AMR][1000 genomes]
rs61592192	1.00[AMR][1000 genomes]
rs61677786	0.85[AMR][1000 genomes]
rs7295258	0.85[AMR][1000 genomes]
rs73406966	1.00[AMR][1000 genomes]
rs73406997	1.00[AMR][1000 genomes]
rs73408803	1.00[AMR][1000 genomes]
rs73408810	1.00[AMR][1000 genomes]
rs73408812	1.00[AMR][1000 genomes]
rs73408818	0.85[AMR][1000 genomes]
rs73408820	0.85[AMR][1000 genomes]
rs73408832	0.85[AMR][1000 genomes]
rs73408835	0.85[AMR][1000 genomes]
rs73408838	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408846	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408890	0.85[AMR][1000 genomes]
rs73408892	0.85[AMR][1000 genomes]
rs73408893	0.85[AMR][1000 genomes]
rs73408894	0.85[AMR][1000 genomes]
rs73408899	0.85[AMR][1000 genomes]
rs73411006	0.85[AMR][1000 genomes]
rs73411009	0.85[AMR][1000 genomes]
rs73411011	0.85[AMR][1000 genomes]
rs73411014	0.85[AMR][1000 genomes]
rs73411015	0.85[AMR][1000 genomes]
rs73411017	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411018	0.85[AMR][1000 genomes]
rs73411027	0.85[AMR][1000 genomes]
rs73411033	1.00[AMR][1000 genomes]
rs73411041	1.00[AMR][1000 genomes]
rs73411043	1.00[AMR][1000 genomes]
rs73411057	1.00[AMR][1000 genomes]
rs73411058	1.00[AMR][1000 genomes]
rs73411063	1.00[AMR][1000 genomes]
rs752164	1.00[AMR][1000 genomes]
rs7971535	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123451000-123453000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:123451000-123453400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:123451000-123453600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:123451000-123454000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:123451000-123454000	Weak transcription	Fetal Lung	lung
6	chr12:123451000-123455800	Enhancers	Fetal Brain Male	brain
7	chr12:123451000-123458600	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:123451400-123453400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:123451400-123453600	Weak transcription	Brain Substantia Nigra	brain
10	chr12:123451400-123454000	Weak transcription	Fetal Heart	heart
11	chr12:123451400-123454200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:123451400-123457600	Weak transcription	Dnd41	blood
13	chr12:123451400-123458200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr12:123451400-123458400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:123451400-123458400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:123451400-123458400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:123451400-123458400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:123451400-123458400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:123451400-123458400	Weak transcription	Brain Anterior Caudate	brain
20	chr12:123451400-123458400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:123451400-123458400	Weak transcription	Brain Germinal Matrix	brain
22	chr12:123451400-123458400	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:123451400-123458600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:123451400-123458600	Weak transcription	Right Atrium	heart
25	chr12:123451400-123458600	Weak transcription	Thymus	Thymus
26	chr12:123451600-123452400	Enhancers	Colonic Mucosa	Colon
27	chr12:123451600-123452800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:123451600-123452800	Weak transcription	Fetal Thymus	thymus
29	chr12:123451600-123452800	Weak transcription	NHEK	skin
30	chr12:123451600-123453600	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:123451600-123453600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:123451600-123454000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:123451600-123455600	Enhancers	Fetal Brain Female	brain
34	chr12:123451600-123457600	Weak transcription	Liver	Liver
35	chr12:123451600-123458200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr12:123451600-123458400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:123451600-123458400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:123451600-123458400	Weak transcription	Adipose Nuclei	Adipose
39	chr12:123451600-123458400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:123451600-123458400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:123451600-123458600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr12:123451600-123458600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:123451600-123458600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr12:123451600-123458600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr12:123451600-123458800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:123451800-123452400	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr12:123451800-123452800	Weak transcription	HMEC	breast
48	chr12:123451800-123453200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:123451800-123453400	Weak transcription	Pancreas	Pancrea
50	chr12:123451800-123454000	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links