Variant report

Variant	rs9559839
Chromosome Location	chr13:111188183-111188184
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:111100852..111102646-chr13:111187472..111189317,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2148079	0.92[ASN][1000 genomes]
rs2148080	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2391835	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2391836	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2391838	0.89[ASN][1000 genomes]
rs2391839	0.94[ASN][1000 genomes]
rs2391840	0.94[ASN][1000 genomes]
rs2391841	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477910	0.88[ASN][1000 genomes]
rs2477911	0.88[ASN][1000 genomes]
rs2479431	0.88[ASN][1000 genomes]
rs2479434	0.88[ASN][1000 genomes]
rs34890574	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35691072	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs377380	0.89[ASN][1000 genomes]
rs394559	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4267185	0.92[ASN][1000 genomes]
rs4268628	0.92[ASN][1000 genomes]
rs4393429	0.92[ASN][1000 genomes]
rs4448791	0.92[ASN][1000 genomes]
rs6492282	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7140104	0.87[ASN][1000 genomes]
rs7339017	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7339377	0.87[ASN][1000 genomes]
rs9515251	0.86[ASN][1000 genomes]
rs9515252	0.85[ASN][1000 genomes]
rs9521823	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9521824	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9521825	0.88[ASN][1000 genomes]
rs9521826	0.88[ASN][1000 genomes]
rs9588184	0.96[EUR][1000 genomes];0.94[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
rs9559839	RAB20	cis	Thyroid	GTEx

Chromatin state (count:60 , 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	chr13:111167000-111190800	Weak transcription	Fetal Kidney	kidney
3	chr13:111180000-111188200	Weak transcription	Brain Anterior Caudate	brain
4	chr13:111180200-111189400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr13:111180400-111189600	Weak transcription	Colonic Mucosa	Colon
6	chr13:111181400-111190800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr13:111182000-111192200	Weak transcription	Fetal Heart	heart
8	chr13:111182200-111193400	Weak transcription	Aorta	Aorta
9	chr13:111182400-111189800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr13:111182400-111193800	Weak transcription	HepG2	liver
11	chr13:111182400-111203600	Weak transcription	Brain Substantia Nigra	brain
12	chr13:111183000-111191400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr13:111183400-111190400	Strong transcription	Fetal Intestine Small	intestine
14	chr13:111183600-111188400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr13:111184000-111193200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr13:111184000-111199600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr13:111184000-111211800	Weak transcription	HMEC	breast
18	chr13:111184200-111189600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:111184200-111193200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr13:111184200-111196400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr13:111184200-111197000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:111184600-111209800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr13:111185200-111188600	Enhancers	Placenta	Placenta
24	chr13:111185600-111188200	Weak transcription	GM12878-XiMat	blood
25	chr13:111185800-111190400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr13:111185800-111191000	Weak transcription	Stomach Mucosa	stomach
27	chr13:111185800-111193600	Weak transcription	Colon Smooth Muscle	Colon
28	chr13:111186200-111188200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:111186200-111188800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr13:111186400-111188400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr13:111186400-111193200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr13:111186600-111192400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr13:111186800-111188400	Weak transcription	Gastric	stomach
34	chr13:111186800-111190000	Weak transcription	Ovary	ovary
35	chr13:111186800-111191400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr13:111186800-111192200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr13:111187000-111189600	Weak transcription	Liver	Liver
38	chr13:111187600-111188600	Strong transcription	Lung	lung
39	chr13:111187600-111188800	Genic enhancers	Pancreas	Pancrea
40	chr13:111187600-111189000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:111187600-111189000	Strong transcription	Fetal Intestine Large	intestine
42	chr13:111187600-111189000	Strong transcription	Fetal Stomach	stomach
43	chr13:111187800-111188200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr13:111187800-111188200	Enhancers	Brain Hippocampus Middle	brain
45	chr13:111187800-111188200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr13:111187800-111188400	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr13:111187800-111188600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr13:111187800-111189000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr13:111188000-111188200	Enhancers	Right Atrium	heart
50	chr13:111188000-111188200	Enhancers	Skeletal Muscle Female	skeletal muscle

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