Variant report

Variant	rs13078854
Chromosome Location	chr3:45861932-45861933
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	chr3:45734225..45736737-chr3:45860844..45863689,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10490770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13071258	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13081482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13092887	0.83[AMR][1000 genomes]
rs17712877	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17713054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17763537	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17763569	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17763742	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34288077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34326463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34668658	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35044562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35081325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35508621	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35624553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35652899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35731912	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35896106	0.84[EUR][1000 genomes]
rs67959919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71325088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72893671	0.92[EUR][1000 genomes]
rs73064425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73064431	0.80[EUR][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv3796	chr3:45850961-45886045	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45847800-45871400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:45848000-45864400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:45849400-45864800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:45849400-45875200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:45849600-45862400	Weak transcription	Fetal Lung	lung
6	chr3:45849800-45871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:45850200-45862200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:45850200-45866200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:45850200-45867800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:45850600-45868200	Weak transcription	Spleen	Spleen
11	chr3:45856000-45862600	Weak transcription	Adipose Nuclei	Adipose
12	chr3:45857800-45862800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:45857800-45863600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:45857800-45871600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:45858000-45862000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:45858000-45862600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:45858000-45882600	Weak transcription	A549	lung
18	chr3:45858200-45862600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:45858200-45863600	Weak transcription	Lung	lung
20	chr3:45858400-45866000	Weak transcription	Fetal Brain Male	brain
21	chr3:45858400-45868400	Weak transcription	Fetal Kidney	kidney
22	chr3:45858400-45881200	Strong transcription	Dnd41	blood
23	chr3:45859400-45862200	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:45859400-45862400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:45859400-45862400	Weak transcription	Brain Substantia Nigra	brain
26	chr3:45859400-45865000	Strong transcription	Brain Germinal Matrix	brain
27	chr3:45859400-45866000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:45859400-45868400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:45859600-45862800	Weak transcription	Primary B cells from cord blood	blood
30	chr3:45859600-45866000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:45859800-45871400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr3:45860000-45862000	Enhancers	Psoas Muscle	Psoas
33	chr3:45860000-45863600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:45860000-45863600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:45860000-45864800	Strong transcription	Fetal Stomach	stomach
36	chr3:45860000-45880000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:45860000-45882400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:45860200-45862000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:45860200-45867600	Weak transcription	GM12878-XiMat	blood
40	chr3:45860400-45862200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:45860400-45862800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:45860400-45862800	Weak transcription	NH-A	brain
43	chr3:45860400-45863200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:45860400-45863400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:45860400-45863800	Weak transcription	Ovary	ovary
46	chr3:45860400-45864400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:45860400-45864800	Strong transcription	Thymus	Thymus
48	chr3:45860400-45867800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:45860400-45868000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:45860400-45868200	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links