Variant report

Variant	rs330558
Chromosome Location	chr13:111278526-111278527
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:111270726..111272560-chr13:111277400..111279622,2	MCF-7	breast:
2	chr13:111248805..111250322-chr13:111277318..111279178,2	MCF-7	breast:
3	chr13:111265898..111273230-chr13:111273500..111281065,16	MCF-7	breast:
4	chr13:111278124..111281264-chr13:111364873..111369262,5	MCF-7	breast:
5	chr13:111266306..111273367-chr13:111274094..111280494,12	K562	blood:
6	chr13:111277493..111279466-chr13:111365604..111368076,3	K562	blood:
7	chr13:111277332..111280156-chr13:111289105..111290945,2	MCF-7	breast:
8	chr13:111266604..111270536-chr13:111275017..111281975,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000153487	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000213995	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2765346	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766501	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2986321	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs330550	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs330554	0.94[ASN][1000 genomes]
rs330556	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330563	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs330564	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs330566	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs392660	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403908	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs424649	0.91[AMR][1000 genomes]
rs441805	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61970485	0.85[EUR][1000 genomes]
rs7394	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
4	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS 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	25 gene(s)	inside rSNPs	diseases
8	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
12	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
14	nsv563123	chr13:111237260-111292044	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv525124	chr13:111261267-111280002	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
16	nsv563124	chr13:111261267-111300943	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
17	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs330558	AL139385.1	cis	Muscle Skeletal	GTEx
rs330558	CARKD	cis	Whole Blood	GTEx
rs330558	CARKD	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111269000-111287000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:111269400-111286600	Weak transcription	Fetal Brain Male	brain
3	chr13:111269400-111287200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr13:111269600-111279800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr13:111270400-111279800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:111270400-111280200	Weak transcription	Fetal Heart	heart
7	chr13:111270400-111282800	Weak transcription	Fetal Kidney	kidney
8	chr13:111270800-111279800	Weak transcription	NH-A	brain
9	chr13:111270800-111296800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr13:111271200-111287000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr13:111271400-111281400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:111271600-111281600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr13:111273400-111281200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr13:111274400-111284400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr13:111274600-111278800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr13:111274600-111278800	Strong transcription	Fetal Thymus	thymus
17	chr13:111274600-111279200	Strong transcription	Right Ventricle	heart
18	chr13:111274600-111279800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr13:111274600-111281200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr13:111274600-111281400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr13:111274600-111281600	Strong transcription	Brain Anterior Caudate	brain
22	chr13:111274600-111281800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr13:111274600-111282200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr13:111274600-111282200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr13:111274600-111282400	Strong transcription	NHLF	lung
26	chr13:111274600-111283600	Strong transcription	Thymus	Thymus
27	chr13:111274600-111284200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr13:111274600-111284200	Strong transcription	Adipose Nuclei	Adipose
29	chr13:111274600-111284200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr13:111274600-111284400	Strong transcription	Placenta	Placenta
31	chr13:111274600-111284400	Strong transcription	Dnd41	blood
32	chr13:111274600-111285000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr13:111274800-111278800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr13:111274800-111280200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr13:111274800-111284000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr13:111274800-111284200	Strong transcription	Primary T cells from cord blood	blood
37	chr13:111274800-111284400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:111274800-111284400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:111275000-111281600	Strong transcription	Fetal Brain Female	brain
40	chr13:111275400-111279200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr13:111275600-111287400	Weak transcription	K562	blood
42	chr13:111275800-111278600	Weak transcription	HMEC	breast
43	chr13:111275800-111279200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr13:111275800-111279200	Weak transcription	NHEK	skin
45	chr13:111275800-111279800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr13:111275800-111280000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr13:111275800-111280600	Weak transcription	NHDF-Ad	bronchial
48	chr13:111275800-111281800	Weak transcription	HSMMtube	muscle
49	chr13:111276000-111278600	Weak transcription	HSMM	muscle
50	chr13:111276000-111279400	Weak transcription	Rectal Smooth Muscle	rectum

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