Variant report

Variant	rs6013838
Chromosome Location	chr20:52548367-52548368
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:52583555..52586146-chr20:52548216..52550675,2	MCF-7	breast:
2	chr20:52367670..52370398-chr20:52548161..52552939,6	K562	blood:
3	chr20:52354654..52356285-chr20:52547034..52549046,2	K562	blood:
4	chr17:59936062..59938856-chr20:52546755..52548819,2	MCF-7	breast:
5	chr20:52546704..52548602-chr20:55839766..55842588,3	MCF-7	breast:
6	chr17:56706895..56708629-chr20:52546888..52548442,2	MCF-7	breast:
7	chr20:52544141..52550658-chr20:55820732..55827450,8	MCF-7	breast:
8	chr20:52547224..52551169-chr20:55839983..55844591,5	MCF-7	breast:
9	chr20:52546661..52548666-chr20:52705907..52707534,2	MCF-7	breast:
10	chr20:52532392..52535656-chr20:52545674..52551256,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction
ENSG00000167767	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16998572	0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.96[ASN][1000 genomes]
rs16998584	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4809945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4811485	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
3	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6013838	NCRNA00200	trans	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52534200-52550200	Weak transcription	Fetal Thymus	thymus
2	chr20:52535200-52550000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:52538400-52553400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr20:52543200-52550400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr20:52543200-52550600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr20:52543400-52550600	Weak transcription	Fetal Kidney	kidney
7	chr20:52543600-52550000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr20:52543600-52550400	Weak transcription	Placenta	Placenta
9	chr20:52543600-52551000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr20:52543600-52556000	Weak transcription	Aorta	Aorta
11	chr20:52543800-52550000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr20:52543800-52550200	Weak transcription	Fetal Muscle Leg	muscle
13	chr20:52543800-52550400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr20:52543800-52551200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr20:52543800-52555000	Weak transcription	Stomach Mucosa	stomach
16	chr20:52544400-52550000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr20:52544600-52549800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr20:52544800-52552000	Weak transcription	Lung	lung
19	chr20:52545600-52548800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr20:52545800-52548800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr20:52545800-52548800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr20:52546200-52548800	Flanking Active TSS	GM12878-XiMat	blood
23	chr20:52546200-52549200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr20:52546600-52549000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr20:52546800-52548400	Enhancers	NHEK	skin
26	chr20:52547000-52548400	Enhancers	A549	lung
27	chr20:52547400-52550200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr20:52547600-52550000	Weak transcription	Primary B cells from cord blood	blood
29	chr20:52547600-52550000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr20:52547600-52550000	Weak transcription	K562	blood
31	chr20:52547600-52550200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr20:52547600-52550200	Weak transcription	HSMMtube	muscle
33	chr20:52547600-52550200	Weak transcription	NHDF-Ad	bronchial
34	chr20:52547600-52550600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr20:52547600-52550800	Weak transcription	NHLF	lung
36	chr20:52547600-52551200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr20:52547800-52550200	Weak transcription	HSMM	muscle
38	chr20:52547800-52550200	Weak transcription	Osteobl	bone
39	chr20:52547800-52550400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr20:52547800-52550800	Weak transcription	HMEC	breast
41	chr20:52547800-52550800	Weak transcription	NH-A	brain
42	chr20:52547800-52551000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr20:52548000-52550200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr20:52548000-52550200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr20:52548000-52550600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr20:52548000-52551000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr20:52548200-52548400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr20:52548200-52548800	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links