Variant report

Variant	rs9332025
Chromosome Location	chr13:49080376-49080377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49075530..49077233-chr13:49077933..49080570,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10076	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs10467381	0.83[AMR][1000 genomes]
rs11840819	0.83[AMR][1000 genomes]
rs11842402	0.83[AMR][1000 genomes]
rs13378245	0.83[AMR][1000 genomes]
rs17071695	1.00[CHD][hapmap]
rs17071917	0.83[AMR][1000 genomes]
rs174858	1.00[CHD][hapmap]
rs198617	1.00[CHD][hapmap]
rs198618	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs2804085	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs2804088	0.82[MEX][hapmap]
rs2804091	0.82[MEX][hapmap]
rs2854361	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs3020646	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs411862	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs4151590	1.00[CHD][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes]
rs449268	1.00[CHD][hapmap]
rs7322110	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7332631	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs7984270	0.83[AMR][1000 genomes]
rs7990103	0.94[AMR][1000 genomes]
rs9316386	1.00[CHD][hapmap]
rs9316390	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316391	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316392	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs9316396	1.00[CHD][hapmap]
rs9316403	0.83[AMR][1000 genomes]
rs9316404	0.93[AMR][1000 genomes]
rs9332036	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9332053	1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs9332066	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9591163	0.82[AMR][1000 genomes]
rs9591167	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591170	0.83[AMR][1000 genomes]
rs9591171	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9591174	0.83[AMR][1000 genomes]
rs9591175	0.83[AMR][1000 genomes]
rs9595894	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[AMR][1000 genomes]
rs9595909	0.94[AMR][1000 genomes]
rs9595910	0.94[AMR][1000 genomes]
rs9595913	0.89[EUR][1000 genomes]
rs9595917	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9332025	RCBTB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:49063000-49087800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:49067000-49084200	Weak transcription	Ovary	ovary
4	chr13:49067200-49105200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr13:49067200-49105400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:49067800-49098000	Weak transcription	Right Ventricle	heart
7	chr13:49068000-49105600	Weak transcription	Gastric	stomach
8	chr13:49068200-49102600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr13:49068400-49081000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr13:49071200-49105600	Weak transcription	Fetal Brain Male	brain
11	chr13:49071800-49086200	Strong transcription	Fetal Stomach	stomach
12	chr13:49071800-49105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr13:49072000-49088400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr13:49072200-49085800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr13:49072200-49095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:49072400-49080400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr13:49073200-49085800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr13:49073600-49087800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr13:49073800-49081200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr13:49074800-49083000	Weak transcription	Fetal Intestine Small	intestine
21	chr13:49075400-49080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr13:49075400-49085800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr13:49075600-49093400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr13:49075600-49095200	Weak transcription	Fetal Intestine Large	intestine
25	chr13:49075800-49080400	Weak transcription	NHLF	lung
26	chr13:49075800-49086000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:49075800-49088400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:49075800-49093200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr13:49076000-49083000	Weak transcription	Fetal Lung	lung
30	chr13:49076000-49084800	Weak transcription	Liver	Liver
31	chr13:49076000-49085800	Weak transcription	Fetal Kidney	kidney
32	chr13:49076600-49084800	Weak transcription	Brain Germinal Matrix	brain
33	chr13:49076600-49097400	Weak transcription	Pancreas	Pancrea
34	chr13:49077000-49085800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:49077400-49080600	Weak transcription	Fetal Brain Female	brain
36	chr13:49077600-49081600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr13:49077800-49081600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr13:49078000-49081600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr13:49078000-49084400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr13:49078200-49081400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr13:49078200-49081600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr13:49078200-49081600	Enhancers	Fetal Thymus	thymus
43	chr13:49078200-49083400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr13:49078600-49081600	Enhancers	Right Atrium	heart
45	chr13:49078600-49082000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr13:49078600-49082200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr13:49078600-49083000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr13:49078600-49083200	Enhancers	HMEC	breast
49	chr13:49078800-49081000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr13:49078800-49081400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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