Variant report

Variant	rs418543
Chromosome Location	chr13:111179796-111179797
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:111175089..111177508-chr13:111178295..111180453,3	MCF-7	breast:
2	chr13:111159240..111160758-chr13:111178996..111181011,2	K562	blood:
3	chr13:111178399..111181198-chr13:111366491..111368547,2	MCF-7	breast:
4	chr13:111160160..111164294-chr13:111174560..111180121,5	MCF-7	breast:
5	chr13:111175845..111178130-chr13:111179058..111181317,2	K562	blood:
6	chr13:111108088..111108850-chr13:111179257..111180150,2	K562	blood:
7	chr13:111178113..111180928-chr13:111206960..111210358,3	MCF-7	breast:
8	chr13:111176916..111182382-chr13:111206819..111214349,14	MCF-7	breast:
9	chr13:111178065..111180954-chr13:111183980..111185741,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232814	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000134871	Chromatin interaction
ENSG00000139832	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2025904	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71419777	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9515246	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1046291	chr13:111125747-111257861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking 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	16 gene(s)	inside rSNPs	diseases
5	nsv1045143	chr13:111126822-111242791	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs418543	C13orf29	cis	lymphoblastoid	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111160800-111209600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr13:111165400-111179800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr13:111167000-111190800	Weak transcription	Fetal Kidney	kidney
4	chr13:111173000-111180000	Enhancers	Right Atrium	heart
5	chr13:111173400-111183200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr13:111173800-111180000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:111174000-111179800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:111175200-111182000	Enhancers	Fetal Heart	heart
9	chr13:111175400-111180200	Enhancers	Fetal Muscle Leg	muscle
10	chr13:111176000-111180400	Enhancers	Left Ventricle	heart
11	chr13:111176000-111182400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr13:111176000-111185800	Enhancers	Stomach Mucosa	stomach
13	chr13:111176200-111182000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr13:111176400-111182400	Enhancers	Adipose Nuclei	Adipose
15	chr13:111176400-111182400	Enhancers	Pancreas	Pancrea
16	chr13:111176600-111180000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr13:111176600-111180400	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr13:111176600-111180600	Enhancers	Lung	lung
19	chr13:111176600-111182000	Enhancers	Fetal Intestine Large	intestine
20	chr13:111176800-111180400	Enhancers	Ovary	ovary
21	chr13:111176800-111180600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr13:111177000-111180400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr13:111177200-111179800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr13:111177200-111180400	Enhancers	Stomach Smooth Muscle	stomach
25	chr13:111177200-111181200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:111177200-111182400	Enhancers	Liver	Liver
27	chr13:111177400-111180000	Enhancers	Right Ventricle	heart
28	chr13:111177400-111180600	Enhancers	H1 Cell Line	embryonic stem cell
29	chr13:111177400-111182200	Enhancers	Placenta	Placenta
30	chr13:111177600-111180200	Enhancers	Hela-S3	cervix
31	chr13:111177600-111182000	Weak transcription	Brain Substantia Nigra	brain
32	chr13:111178000-111180400	Enhancers	Small Intestine	intestine
33	chr13:111178000-111181400	Weak transcription	Brain Hippocampus Middle	brain
34	chr13:111178200-111181000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr13:111178400-111180000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr13:111178400-111180400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:111178600-111179800	Weak transcription	Esophagus	oesophagus
38	chr13:111178600-111180200	Enhancers	Gastric	stomach
39	chr13:111178600-111181000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr13:111178600-111181200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr13:111178600-111183000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr13:111178600-111188000	Weak transcription	Primary B cells from cord blood	blood
43	chr13:111179000-111180000	Enhancers	Psoas Muscle	Psoas
44	chr13:111179000-111182400	Enhancers	HepG2	liver
45	chr13:111179200-111179800	Enhancers	Brain Cingulate Gyrus	brain
46	chr13:111179200-111180200	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr13:111179200-111180400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr13:111179200-111180400	Enhancers	Aorta	Aorta
49	chr13:111179200-111182600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:111179200-111183600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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