Variant report

Variant	rs9515252
Chromosome Location	chr13:111199555-111199556
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111180150..111181818-chr13:111197794..111200126,2	MCF-7	breast:
2	chr13:111198748..111201461-chr13:111207040..111209590,2	K562	blood:
3	chr13:111198043..111201008-chr13:111205585..111207833,2	MCF-7	breast:
4	chr13:111199528..111201235-chr13:111211213..111213548,2	MCF-7	breast:
5	chr13:111199454..111201180-chr13:111212075..111214723,2	MCF-7	breast:
6	chr13:111189757..111192699-chr13:111197488..111200352,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139832	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs2148079	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2148080	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391835	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2391836	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2391838	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2391839	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2391840	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2391841	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2477910	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2477911	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2479431	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2479434	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs331596	0.90[EUR][1000 genomes]
rs331602	0.81[EUR][1000 genomes]
rs34890574	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35691072	0.83[ASN][1000 genomes]
rs377380	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs394559	0.85[ASN][1000 genomes]
rs4267185	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4268628	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4393429	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4448791	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6492282	0.85[ASN][1000 genomes]
rs7140104	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7339017	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7339377	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9515251	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9521823	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9521824	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9521825	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9521826	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9521836	0.82[EUR][1000 genomes]
rs9521838	0.83[EUR][1000 genomes]
rs9521839	0.83[EUR][1000 genomes]
rs9559839	0.85[ASN][1000 genomes]
rs9588184	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
rs9515252	RAB20	cis	Thyroid	GTEx

Chromatin state (count:69 , 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	chr13:111182400-111203600	Weak transcription	Brain Substantia Nigra	brain
3	chr13:111184000-111199600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr13:111184000-111211800	Weak transcription	HMEC	breast
5	chr13:111184600-111209800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:111188400-111203600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr13:111189000-111201600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr13:111191200-111213000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr13:111191400-111203600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr13:111191400-111207200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr13:111192200-111212000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr13:111194200-111203800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr13:111194400-111203600	Weak transcription	Fetal Stomach	stomach
14	chr13:111194400-111203800	Weak transcription	Psoas Muscle	Psoas
15	chr13:111194400-111212000	Weak transcription	K562	blood
16	chr13:111195000-111202800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr13:111195200-111203600	Weak transcription	Right Ventricle	heart
18	chr13:111195400-111203200	Weak transcription	Fetal Heart	heart
19	chr13:111195400-111211400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr13:111196400-111201000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:111197200-111203000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:111197200-111211800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr13:111197800-111199800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr13:111197800-111204200	Enhancers	Pancreas	Pancrea
25	chr13:111197800-111208400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr13:111198200-111200200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr13:111198200-111200400	Enhancers	Stomach Mucosa	stomach
28	chr13:111198400-111200200	Enhancers	Ovary	ovary
29	chr13:111198400-111200200	Enhancers	NH-A	brain
30	chr13:111198400-111201200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr13:111198600-111199800	Enhancers	Osteobl	bone
32	chr13:111198600-111200000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr13:111198600-111200400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr13:111198800-111199600	Enhancers	HepG2	liver
35	chr13:111198800-111200000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr13:111198800-111200000	Enhancers	Gastric	stomach
37	chr13:111198800-111200000	Enhancers	Small Intestine	intestine
38	chr13:111198800-111200000	Enhancers	A549	lung
39	chr13:111198800-111200200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr13:111198800-111200200	Enhancers	Left Ventricle	heart
41	chr13:111198800-111200200	Enhancers	HUVEC	blood vessel
42	chr13:111198800-111200400	Enhancers	Placenta	Placenta
43	chr13:111198800-111200400	Enhancers	Right Atrium	heart
44	chr13:111198800-111203000	Strong transcription	Fetal Intestine Small	intestine
45	chr13:111199000-111200000	Enhancers	Colonic Mucosa	Colon
46	chr13:111199000-111200200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr13:111199200-111199800	Genic enhancers	Monocytes-CD14+_RO01746	blood
48	chr13:111199200-111200000	Genic enhancers	Lung	lung
49	chr13:111199200-111200200	Genic enhancers	Adipose Nuclei	Adipose
50	chr13:111199200-111201400	Strong transcription	Fetal Intestine Large	intestine

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