Variant report

Variant	rs55739420
Chromosome Location	chr6:13262993-13262994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13258411..13260332-chr6:13262942..13264802,3	K562	blood:
2	chr6:13258411..13260332-chr6:13262942..13264673,2	K562	blood:
3	chr6:13259737..13263124-chr6:13265994..13271257,6	K562	blood:
4	chr6:13258559..13263124-chr6:13265994..13271116,8	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11757292	0.96[EUR][1000 genomes]
rs11758225	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4464796	0.96[EUR][1000 genomes]
rs55903603	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56380716	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57728205	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs578290	0.83[EUR][1000 genomes]
rs58425216	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58875474	0.96[EUR][1000 genomes]
rs6458744	0.92[EUR][1000 genomes]
rs6928672	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73725628	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73725649	0.96[EUR][1000 genomes]
rs7757265	0.96[EUR][1000 genomes]
rs7769621	0.85[EUR][1000 genomes]
rs7770755	0.85[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13234600-13267200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:13248800-13266600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:13249000-13266000	Weak transcription	Fetal Brain Female	brain
4	chr6:13249200-13272200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
6	chr6:13253000-13264200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr6:13254000-13265400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:13256400-13266400	Weak transcription	Aorta	Aorta
9	chr6:13256600-13266000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:13256600-13267000	Weak transcription	Fetal Stomach	stomach
11	chr6:13256600-13268800	Weak transcription	Right Ventricle	heart
12	chr6:13256600-13272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:13256600-13273200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea
15	chr6:13257400-13263000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:13258000-13263000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:13258600-13263400	Flanking Active TSS	GM12878-XiMat	blood
18	chr6:13258800-13272200	Weak transcription	Left Ventricle	heart
19	chr6:13259400-13267400	Weak transcription	Fetal Heart	heart
20	chr6:13259600-13263400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr6:13259800-13266800	Weak transcription	K562	blood
22	chr6:13260200-13263600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:13260400-13263600	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr6:13260600-13266600	Weak transcription	Brain Germinal Matrix	brain
25	chr6:13261000-13263000	Weak transcription	Brain Substantia Nigra	brain
26	chr6:13261000-13263200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr6:13261000-13263400	Enhancers	Primary hematopoietic stem cells	blood
28	chr6:13261000-13265800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:13261000-13266600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:13261000-13268800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:13261200-13263000	Enhancers	Fetal Thymus	thymus
32	chr6:13261400-13266400	Weak transcription	Lung	lung
33	chr6:13261400-13272200	Weak transcription	Brain Angular Gyrus	brain
34	chr6:13261400-13272200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:13261400-13273000	Weak transcription	Adipose Nuclei	Adipose
36	chr6:13261600-13272200	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:13261800-13263000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:13262200-13263400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:13262200-13263400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:13262400-13263400	Enhancers	Brain Anterior Caudate	brain
41	chr6:13262600-13272400	Enhancers	Primary B cells from peripheral blood	blood
42	chr6:13262600-13272800	Weak transcription	Primary T cells from cord blood	blood
43	chr6:13262800-13263200	Weak transcription	Spleen	Spleen
44	chr6:13262800-13263400	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr6:13262800-13263800	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links