Variant report

Variant	rs12747275
Chromosome Location	chr1:93426541-93426542
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:93425993..93428373-chr1:93433568..93436256,2	MCF-7	breast:
2	chr1:93426062..93426867-chr1:93459810..93460332,2	MCF-7	breast:
3	chr1:93296297..93299381-chr1:93425183..93428047,4	K562	blood:
4	chr1:93296356..93298770-chr1:93426282..93429088,3	MCF-7	breast:
5	chr1:93324139..93325155-chr1:93425615..93426899,9	MCF-7	breast:
6	chr1:93425058..93429733-chr1:93431759..93435608,8	K562	blood:
7	chr1:93426343..93426854-chr20:42285915..42286690,2	NB4	blood:
8	chr1:93378943..93379622-chr1:93425899..93426864,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252121	Chromatin interaction
ENSG00000122406	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10874752	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164814	1.00[JPT][hapmap]
rs11164820	1.00[JPT][hapmap]
rs11164838	0.82[ASN][1000 genomes]
rs11164848	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164849	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11586570	1.00[JPT][hapmap]
rs12081675	1.00[JPT][hapmap]
rs12092304	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728322	1.00[JPT][hapmap]
rs1854797	1.00[JPT][hapmap]
rs2893226	1.00[JPT][hapmap]
rs35183060	1.00[JPT][hapmap]
rs4847386	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847389	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs514235	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs521428	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs606344	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs619784	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs641462	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6604026	1.00[JPT][hapmap]
rs660870	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6671078	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6671268	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6681240	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681345	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7514280	1.00[JPT][hapmap]
rs7521417	1.00[JPT][hapmap]
rs753391	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs770884	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	esv3339713	chr1:93425789-93428737	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12747275	FAM69A	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93425200-93428000	Active TSS	Brain Hippocampus Middle	brain
2	chr1:93425200-93428000	Active TSS	NHDF-Ad	bronchial
3	chr1:93425200-93428200	Active TSS	Liver	Liver
4	chr1:93425200-93428200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:93425200-93428200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:93425200-93428200	Active TSS	Brain Substantia Nigra	brain
7	chr1:93425400-93428200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:93425400-93428200	Active TSS	Brain Angular Gyrus	brain
9	chr1:93425400-93428200	Active TSS	Brain Anterior Caudate	brain
10	chr1:93425600-93426600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr1:93425600-93426600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:93425600-93426600	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr1:93425600-93426600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
14	chr1:93425600-93426600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr1:93425600-93427800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:93425600-93427800	Active TSS	Brain Cingulate Gyrus	brain
17	chr1:93425600-93427800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr1:93425600-93428000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:93425600-93428000	Active TSS	Fetal Brain Female	brain
20	chr1:93425600-93428000	Active TSS	Pancreas	Pancrea
21	chr1:93425600-93428200	Active TSS	Colonic Mucosa	Colon
22	chr1:93425600-93428200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr1:93425600-93428400	Active TSS	Aorta	Aorta
24	chr1:93425800-93426600	Flanking Active TSS	Placenta	Placenta
25	chr1:93425800-93426600	Flanking Active TSS	K562	blood
26	chr1:93425800-93426600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr1:93425800-93426800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:93425800-93427600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:93425800-93427600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:93425800-93427800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:93425800-93427800	Active TSS	Fetal Intestine Small	intestine
32	chr1:93425800-93427800	Active TSS	Rectal Smooth Muscle	rectum
33	chr1:93425800-93427800	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr1:93425800-93427800	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr1:93425800-93428000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr1:93425800-93428000	Active TSS	Colon Smooth Muscle	Colon
37	chr1:93425800-93428000	Active TSS	Psoas Muscle	Psoas
38	chr1:93425800-93428000	Active TSS	Right Atrium	heart
39	chr1:93425800-93428000	Active TSS	Right Ventricle	heart
40	chr1:93425800-93428200	Active TSS	GM12878-XiMat	blood
41	chr1:93426000-93426600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:93426000-93426600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:93426000-93426600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:93426000-93426600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr1:93426000-93426600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
46	chr1:93426000-93426600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr1:93426000-93426600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:93426000-93426600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:93426000-93426600	Active TSS	Fetal Brain Male	brain
50	chr1:93426000-93426600	Active TSS	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links