Variant report

Variant	rs9535032
Chromosome Location	chr13:49012265-49012266
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	chr13:49002533..49005304-chr13:49011624..49014276,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11839271	0.97[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12430215	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12875750	0.86[CEU][hapmap]
rs1573601	0.86[CEU][hapmap]
rs1894255	0.81[CEU][hapmap]
rs1951775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1981434	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs198563	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs198570	0.83[EUR][1000 genomes]
rs198584	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs198590	0.90[CEU][hapmap]
rs198607	0.81[CEU][hapmap]
rs198612	0.86[CEU][hapmap]
rs198619	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2227311	0.82[YRI][hapmap]
rs2243626	1.00[ASW][hapmap];0.90[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs2248488	0.86[CEU][hapmap]
rs2406935	0.82[EUR][1000 genomes]
rs2897588	0.86[EUR][1000 genomes]
rs3092877	1.00[YRI][hapmap]
rs3818455	0.86[CEU][hapmap]
rs399413	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4151450	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4151510	1.00[YRI][hapmap]
rs4942765	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs520342	0.86[CEU][hapmap]
rs7139578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap]
rs7333360	0.81[EUR][1000 genomes]
rs7984795	0.95[CEU][hapmap]
rs9316369	0.85[CEU][hapmap]
rs9316381	0.90[CEU][hapmap]
rs9316382	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9316388	0.90[CEU][hapmap]
rs9316394	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9316395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9316399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs943278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs943283	0.86[EUR][1000 genomes]
rs9526465	0.95[CEU][hapmap]
rs9526475	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9526479	0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9534998	0.86[CEU][hapmap]
rs9535006	0.85[CEU][hapmap]
rs9535009	0.86[CEU][hapmap]
rs9535015	0.82[EUR][1000 genomes]
rs9535016	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9535018	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9535033	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535035	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9562819	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9568029	0.95[CEU][hapmap]
rs9568036	0.84[MKK][hapmap]
rs9568042	0.93[ASN][1000 genomes]
rs9568043	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs990814	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9535032	ITM2B	cis	lymphoblastoid	seeQTL
rs9535032	ATAD2	trans	parietal	SCAN
rs9535032	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs9535032	LPAR6	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48990800-49030800	Weak transcription	Ovary	ovary
2	chr13:48991400-49013200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr13:48991400-49018600	Weak transcription	Thymus	Thymus
4	chr13:48991400-49019200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:48991400-49030600	Weak transcription	Spleen	Spleen
6	chr13:48991800-49018800	Weak transcription	Fetal Thymus	thymus
7	chr13:48994800-49018000	Weak transcription	Primary B cells from cord blood	blood
8	chr13:48999000-49024400	Weak transcription	Fetal Muscle Leg	muscle
9	chr13:49001400-49022400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr13:49001400-49024600	Weak transcription	Fetal Intestine Small	intestine
11	chr13:49003000-49012600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:49003600-49023200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr13:49006000-49018000	Weak transcription	Dnd41	blood
14	chr13:49006400-49018800	Weak transcription	GM12878-XiMat	blood
15	chr13:49006800-49020200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:49006800-49020400	Weak transcription	HSMMtube	muscle
17	chr13:49006800-49020800	Weak transcription	Hela-S3	cervix
18	chr13:49006800-49030400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr13:49007000-49027600	Weak transcription	Primary T cells from cord blood	blood
20	chr13:49008000-49028600	Weak transcription	HepG2	liver
21	chr13:49008800-49030800	Weak transcription	Placenta	Placenta
22	chr13:49009000-49030600	Weak transcription	Gastric	stomach
23	chr13:49009000-49030600	Weak transcription	Lung	lung
24	chr13:49009400-49012800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr13:49010200-49012800	Enhancers	Stomach Mucosa	stomach
26	chr13:49010800-49012400	Enhancers	Fetal Heart	heart
27	chr13:49010800-49017800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr13:49010800-49017800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr13:49011000-49012400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr13:49011200-49012600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr13:49011200-49028800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr13:49011400-49017800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr13:49011400-49022800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr13:49011800-49017200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr13:49011800-49020400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr13:49011800-49023600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr13:49012000-49016600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr13:49012000-49016800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr13:49012000-49017400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr13:49012000-49018000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr13:49012000-49018000	Weak transcription	Fetal Stomach	stomach
42	chr13:49012000-49018600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr13:49012000-49019400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr13:49012000-49019800	Weak transcription	HUVEC	blood vessel
45	chr13:49012000-49020200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr13:49012000-49020200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr13:49012000-49020400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:49012000-49020400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr13:49012000-49020400	Weak transcription	NHLF	lung
50	chr13:49012000-49020400	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links