Variant report

Variant	rs9332053
Chromosome Location	chr13:49072565-49072566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49065216..49067091-chr13:49070291..49073195,2	K562	blood:
2	chr13:49066305..49068745-chr13:49072101..49074756,2	MCF-7	breast:
3	chr13:49070136..49072576-chr13:49104860..49107906,3	MCF-7	breast:
4	chr13:49068490..49070652-chr13:49071490..49073250,2	K562	blood:

Variant related genes	Relation type
ENSG00000136161	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10076	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes]
rs10467381	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11840819	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11842402	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11842662	0.95[AMR][1000 genomes]
rs13378245	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071917	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071960	0.95[AMR][1000 genomes]
rs171989	0.82[EUR][1000 genomes]
rs174854	0.95[AMR][1000 genomes]
rs198559	0.82[EUR][1000 genomes]
rs198565	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs198566	0.82[EUR][1000 genomes]
rs198567	0.82[EUR][1000 genomes]
rs198572	0.82[EUR][1000 genomes]
rs198573	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs198581	0.90[AMR][1000 genomes]
rs198583	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs198587	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs198600	0.82[EUR][1000 genomes]
rs198601	0.82[EUR][1000 genomes]
rs198613	0.82[EUR][1000 genomes]
rs198616	0.82[EUR][1000 genomes]
rs198617	0.84[LWK][hapmap];0.90[MKK][hapmap];0.82[EUR][1000 genomes]
rs198618	0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[EUR][1000 genomes]
rs198628	0.82[EUR][1000 genomes]
rs198632	0.82[EUR][1000 genomes]
rs198636	0.82[EUR][1000 genomes]
rs2804082	0.82[ASW][hapmap];0.82[MKK][hapmap];0.82[EUR][1000 genomes]
rs2804084	0.82[EUR][1000 genomes]
rs2804085	0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs2804086	0.82[EUR][1000 genomes]
rs2804087	0.82[EUR][1000 genomes]
rs2804088	0.82[MEX][hapmap];0.82[EUR][1000 genomes]
rs2804089	0.82[EUR][1000 genomes]
rs2804091	0.82[MEX][hapmap];0.81[MKK][hapmap]
rs2854361	1.00[MEX][hapmap];0.85[MKK][hapmap]
rs2854363	0.82[EUR][1000 genomes]
rs2854364	0.82[EUR][1000 genomes]
rs2984828	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3020646	1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs411862	0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4151590	1.00[MEX][hapmap]
rs416156	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs428431	0.82[EUR][1000 genomes]
rs547747	0.82[EUR][1000 genomes]
rs7322110	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7332631	1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs7984270	1.00[AMR][1000 genomes]
rs7990103	0.82[EUR][1000 genomes]
rs9316384	0.82[AMR][1000 genomes]
rs9316386	1.00[GIH][hapmap]
rs9316387	0.82[AMR][1000 genomes]
rs9316390	0.83[AMR][1000 genomes]
rs9316391	0.83[AMR][1000 genomes]
rs9316392	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes]
rs9316396	1.00[GIH][hapmap]
rs9316403	1.00[AMR][1000 genomes]
rs9332025	1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs9332036	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332050	0.95[AMR][1000 genomes]
rs9332066	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9562817	0.82[EUR][1000 genomes]
rs9591163	0.82[EUR][1000 genomes]
rs9591167	0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9591170	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9591171	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes]
rs9591174	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9591175	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9595894	1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs9595909	0.82[EUR][1000 genomes]
rs9595910	0.82[EUR][1000 genomes]
rs9595913	0.95[AMR][1000 genomes]
rs9595914	0.82[AMR][1000 genomes]
rs9595917	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9595930	0.95[AMR][1000 genomes]
rs9595936	0.95[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9332053	RCBTB2	cis	lymphoblastoid	seeQTL
rs9332053	LPAR6	cis	lymphoblastoid	seeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49023800-49073800	Weak transcription	NH-A	brain
2	chr13:49034400-49073800	Weak transcription	Esophagus	oesophagus
3	chr13:49035200-49073400	Weak transcription	Fetal Intestine Small	intestine
4	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:49063000-49087800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:49064200-49075200	Weak transcription	Fetal Intestine Large	intestine
7	chr13:49066800-49073200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr13:49066800-49080200	Weak transcription	Colonic Mucosa	Colon
9	chr13:49067000-49072800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:49067000-49074600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr13:49067000-49080200	Weak transcription	Psoas Muscle	Psoas
12	chr13:49067000-49084200	Weak transcription	Ovary	ovary
13	chr13:49067200-49073200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr13:49067200-49074600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:49067200-49079200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr13:49067200-49079600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr13:49067200-49080200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr13:49067200-49105200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr13:49067200-49105400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr13:49067800-49073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:49067800-49074800	Weak transcription	Left Ventricle	heart
22	chr13:49067800-49074800	Weak transcription	NHLF	lung
23	chr13:49067800-49078600	Weak transcription	Placenta	Placenta
24	chr13:49067800-49078600	Weak transcription	Right Atrium	heart
25	chr13:49067800-49078600	Weak transcription	Stomach Mucosa	stomach
26	chr13:49067800-49079400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr13:49067800-49098000	Weak transcription	Right Ventricle	heart
28	chr13:49068000-49075400	Weak transcription	Fetal Kidney	kidney
29	chr13:49068000-49075600	Weak transcription	Pancreas	Pancrea
30	chr13:49068000-49078200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr13:49068000-49078400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr13:49068000-49105600	Weak transcription	Gastric	stomach
33	chr13:49068200-49102600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr13:49068400-49073000	Weak transcription	Osteobl	bone
35	chr13:49068400-49073800	Weak transcription	NHDF-Ad	bronchial
36	chr13:49068400-49074600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:49068400-49081000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr13:49068600-49074600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:49068600-49074600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr13:49068800-49073000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr13:49068800-49073400	Weak transcription	Liver	Liver
42	chr13:49068800-49076400	Weak transcription	Lung	lung
43	chr13:49069000-49072800	Weak transcription	HSMM	muscle
44	chr13:49069000-49073000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr13:49069000-49073200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr13:49069000-49073200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr13:49069000-49074600	Weak transcription	Adipose Nuclei	Adipose
48	chr13:49069400-49073200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr13:49069400-49073200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr13:49070200-49073600	Enhancers	Fetal Thymus	thymus

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