Variant report

Variant	rs541119
Chromosome Location	chr6:13398846-13398847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13398336..13400389-chr6:13402109..13404070,2	K562	blood:
2	chr6:13396704..13399515-chr6:13413657..13416189,2	K562	blood:
3	chr6:13397579..13400126-chr6:13573111..13574727,2	MCF-7	breast:
4	chr6:13354231..13355859-chr6:13396144..13399097,2	K562	blood:
5	chr6:13397740..13400586-chr6:13613823..13615794,2	K562	blood:

Variant related genes	Relation type
ENSG00000225921	Chromatin interaction
ENSG00000261071	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4145561	0.84[YRI][hapmap]
rs493908	0.85[AFR][1000 genomes]
rs495891	0.85[AFR][1000 genomes]
rs511992	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs521835	0.84[AFR][1000 genomes]
rs536607	1.00[AMR][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:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:13394600-13399000	Enhancers	Primary B cells from peripheral blood	blood
3	chr6:13395000-13399000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:13395200-13399000	Enhancers	Primary hematopoietic stem cells	blood
5	chr6:13395200-13399200	Enhancers	Adipose Nuclei	Adipose
6	chr6:13395400-13399000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:13395400-13399000	Enhancers	Spleen	Spleen
8	chr6:13395400-13399200	Enhancers	Psoas Muscle	Psoas
9	chr6:13395400-13399200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr6:13395400-13399200	Enhancers	A549	lung
11	chr6:13395400-13399400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:13395400-13399400	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:13395400-13399600	Enhancers	Left Ventricle	heart
14	chr6:13395600-13399400	Enhancers	Right Ventricle	heart
15	chr6:13395600-13402800	Enhancers	Fetal Heart	heart
16	chr6:13396000-13404400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr6:13396200-13399400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:13396200-13407000	Weak transcription	Gastric	stomach
19	chr6:13396400-13404400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:13396600-13405800	Weak transcription	HepG2	liver
21	chr6:13396800-13404400	Weak transcription	NHLF	lung
22	chr6:13397000-13399000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:13397000-13399000	Enhancers	HMEC	breast
24	chr6:13397000-13399400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:13397000-13404600	Weak transcription	Aorta	Aorta
26	chr6:13397200-13399200	Enhancers	HSMMtube	muscle
27	chr6:13397200-13399800	Enhancers	Brain Cingulate Gyrus	brain
28	chr6:13397200-13400000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:13397600-13399000	Enhancers	Colon Smooth Muscle	Colon
30	chr6:13397600-13399400	Enhancers	Brain Hippocampus Middle	brain
31	chr6:13397800-13399000	Enhancers	Fetal Stomach	stomach
32	chr6:13397800-13399200	Flanking Active TSS	NHEK	skin
33	chr6:13398000-13404400	Weak transcription	Esophagus	oesophagus
34	chr6:13398000-13404600	Weak transcription	Small Intestine	intestine
35	chr6:13398000-13406000	Weak transcription	Lung	lung
36	chr6:13398200-13399000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:13398200-13399200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:13398200-13406800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:13398400-13399200	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr6:13398400-13399200	Enhancers	Brain Angular Gyrus	brain
41	chr6:13398400-13399200	Weak transcription	Right Atrium	heart
42	chr6:13398400-13399400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:13398400-13399400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr6:13398400-13399400	Enhancers	Brain Anterior Caudate	brain
45	chr6:13398400-13399400	Enhancers	Placenta Amnion	Placenta Amnion
46	chr6:13398400-13400600	Enhancers	Stomach Smooth Muscle	stomach
47	chr6:13398400-13400600	Enhancers	GM12878-XiMat	blood
48	chr6:13398400-13400600	Weak transcription	K562	blood
49	chr6:13398400-13400800	Weak transcription	HUVEC	blood vessel
50	chr6:13398400-13407400	Weak transcription	Placenta	Placenta

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