Variant report

Variant	rs9559836
Chromosome Location	chr13:111182151-111182152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111171438..111174386-chr13:111180872..111182991,2	MCF-7	breast:
2	chr13:111176916..111182382-chr13:111206819..111214349,14	MCF-7	breast:
3	chr13:111175360..111178796-chr13:111180023..111183032,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139832	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs4773210	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9515243	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9515247	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9559840	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9634592	0.82[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9559836	DEGS1	cis	Brain Pons	GTEx
rs9559836	CCDC88A	cis	Brain Pons	GTEx

Chromatin state (count:63 , 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	chr13:111173400-111183200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr13:111176000-111182400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr13:111176000-111185800	Enhancers	Stomach Mucosa	stomach
6	chr13:111176400-111182400	Enhancers	Adipose Nuclei	Adipose
7	chr13:111176400-111182400	Enhancers	Pancreas	Pancrea
8	chr13:111177200-111182400	Enhancers	Liver	Liver
9	chr13:111177400-111182200	Enhancers	Placenta	Placenta
10	chr13:111178600-111183000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr13:111178600-111188000	Weak transcription	Primary B cells from cord blood	blood
12	chr13:111179000-111182400	Enhancers	HepG2	liver
13	chr13:111179200-111182600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:111179200-111183600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr13:111179200-111183800	Weak transcription	GM12878-XiMat	blood
16	chr13:111179400-111182400	Genic enhancers	Fetal Intestine Small	intestine
17	chr13:111179600-111182200	Enhancers	Spleen	Spleen
18	chr13:111179600-111182600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr13:111179800-111182200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr13:111179800-111183400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr13:111180000-111183400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr13:111180000-111183400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr13:111180000-111187600	Weak transcription	Fetal Stomach	stomach
24	chr13:111180000-111188000	Weak transcription	Right Ventricle	heart
25	chr13:111180000-111188200	Weak transcription	Brain Anterior Caudate	brain
26	chr13:111180200-111183200	Weak transcription	Colon Smooth Muscle	Colon
27	chr13:111180200-111183800	Weak transcription	Gastric	stomach
28	chr13:111180200-111184000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr13:111180200-111189400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr13:111180400-111183200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr13:111180400-111183600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr13:111180400-111186400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr13:111180400-111189600	Weak transcription	Colonic Mucosa	Colon
34	chr13:111180600-111182400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:111180600-111183400	Weak transcription	Lung	lung
36	chr13:111181000-111182400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr13:111181000-111183800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr13:111181000-111188000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr13:111181200-111182200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr13:111181200-111182200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr13:111181200-111182400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr13:111181400-111182200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:111181400-111182200	Enhancers	Left Ventricle	heart
44	chr13:111181400-111183600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr13:111181400-111184400	Enhancers	Placenta Amnion	Placenta Amnion
46	chr13:111181400-111190800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr13:111181600-111182200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr13:111181600-111182200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr13:111181600-111182200	Enhancers	Aorta	Aorta
50	chr13:111181600-111182200	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links