Variant report

Variant	rs17059017
Chromosome Location	chr13:39602461-39602462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:39601544-39602558	K562	blood:	n/a	n/a
2	MAFK	chr13:39602403-39602620	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:39594195..39597127-chr13:39600978..39605869,5	K562	blood:
2	chr13:39601651..39604089-chr13:39618475..39621236,2	MCF-7	breast:
3	chr13:39599530..39604283-chr13:39604707..39609132,9	K562	blood:
4	chr13:39600178..39602849-chr13:39610760..39613364,3	K562	blood:

Variant related genes	Relation type
PROSER1	TF binding region
ENSG00000188811	Chromatin interaction
ENSG00000120685	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17058950	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs17058955	1.00[AMR][1000 genomes]
rs17058957	1.00[AMR][1000 genomes]
rs17058977	1.00[AMR][1000 genomes]
rs17058982	1.00[AMR][1000 genomes]
rs17058983	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17058988	1.00[AMR][1000 genomes]
rs17059021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17059023	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17059035	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17059072	1.00[YRI][hapmap]
rs61745902	1.00[AMR][1000 genomes]
rs7991750	1.00[AMR][1000 genomes]
rs7993045	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39582000-39608200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:39582400-39605400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr13:39583200-39606600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr13:39584600-39603600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr13:39587800-39608200	Weak transcription	Fetal Brain Male	brain
6	chr13:39588400-39608800	Weak transcription	Stomach Mucosa	stomach
7	chr13:39588600-39608200	Weak transcription	Hela-S3	cervix
8	chr13:39588600-39610400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:39589200-39608400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr13:39589200-39609400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr13:39591200-39608400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:39592200-39602800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:39592400-39606600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr13:39594200-39603000	Strong transcription	Adipose Nuclei	Adipose
15	chr13:39594200-39604000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr13:39594200-39605600	Strong transcription	Dnd41	blood
17	chr13:39594400-39604200	Strong transcription	HUVEC	blood vessel
18	chr13:39594600-39605400	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr13:39594800-39602600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr13:39594800-39602600	Strong transcription	NHDF-Ad	bronchial
21	chr13:39594800-39603000	Strong transcription	Primary B cells from cord blood	blood
22	chr13:39594800-39603000	Strong transcription	Liver	Liver
23	chr13:39594800-39603000	Strong transcription	Fetal Muscle Leg	muscle
24	chr13:39594800-39603000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr13:39594800-39603400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr13:39594800-39603400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr13:39594800-39603400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:39594800-39605400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr13:39594800-39606400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr13:39594800-39608400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr13:39595000-39603000	Strong transcription	Primary hematopoietic stem cells	blood
32	chr13:39595000-39603000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr13:39595000-39603000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr13:39595000-39603000	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr13:39595000-39603000	Strong transcription	Fetal Kidney	kidney
36	chr13:39595000-39603200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr13:39595000-39603800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr13:39595000-39606400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr13:39595000-39606400	Strong transcription	HSMM	muscle
40	chr13:39595000-39606600	Strong transcription	Fetal Thymus	thymus
41	chr13:39595200-39603000	Strong transcription	Osteobl	bone
42	chr13:39595400-39605200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr13:39598000-39603200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr13:39598000-39607800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr13:39598000-39609600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr13:39598200-39602800	Strong transcription	NHEK	skin
47	chr13:39598200-39603400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr13:39598200-39605200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr13:39598200-39606200	Weak transcription	Psoas Muscle	Psoas
50	chr13:39598200-39608800	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links