Variant report

Variant	rs9535038
Chromosome Location	chr13:49142829-49142830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49141688..49143234-chr13:49148647..49150198,2	MCF-7	breast:
2	chr13:49142248..49144143-chr13:49147250..49149323,2	K562	blood:
3	chr13:49115025..49117372-chr13:49140241..49143183,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233456	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11148110	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12855185	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12859099	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12876717	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12877288	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12877954	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1359688	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536396	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1536397	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1808060	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs198563	0.80[EUR][1000 genomes]
rs198570	0.80[EUR][1000 genomes]
rs198584	0.86[EUR][1000 genomes]
rs198590	0.86[EUR][1000 genomes]
rs2104532	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2406935	0.83[EUR][1000 genomes]
rs2407093	0.87[EUR][1000 genomes]
rs2407095	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2897588	0.81[EUR][1000 genomes]
rs3092904	0.86[EUR][1000 genomes]
rs4635233	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7139578	0.86[EUR][1000 genomes]
rs7325719	0.81[EUR][1000 genomes]
rs7329065	0.85[EUR][1000 genomes]
rs7333360	0.84[EUR][1000 genomes]
rs7336379	0.87[EUR][1000 genomes]
rs8002098	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9316381	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9316388	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9316393	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9316394	0.83[EUR][1000 genomes]
rs9316395	0.83[EUR][1000 genomes]
rs9316399	0.83[EUR][1000 genomes]
rs9316407	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9331991	0.81[ASN][1000 genomes]
rs943280	0.91[EUR][1000 genomes]
rs943283	0.81[EUR][1000 genomes]
rs9526479	0.83[EUR][1000 genomes]
rs9526481	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526483	0.97[EUR][1000 genomes]
rs9535042	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535043	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535045	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535046	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535049	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9568047	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568049	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568050	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568051	0.81[EUR][1000 genomes]
rs9634680	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9535038	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49135000-49155000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr13:49137200-49153000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr13:49137400-49145200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr13:49138800-49145600	Weak transcription	HUVEC	blood vessel
5	chr13:49139000-49144800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr13:49139600-49144400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr13:49140000-49144200	Weak transcription	K562	blood
8	chr13:49140800-49146400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:49141000-49145000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:49141200-49147000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr13:49141400-49143400	Enhancers	Stomach Mucosa	stomach
12	chr13:49141400-49144800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr13:49141400-49145800	Enhancers	Fetal Stomach	stomach
14	chr13:49141400-49146200	Enhancers	HepG2	liver
15	chr13:49141400-49146400	Enhancers	Fetal Lung	lung
16	chr13:49141400-49146600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr13:49141800-49144000	Weak transcription	Fetal Kidney	kidney
18	chr13:49141800-49144200	Bivalent Enhancer	Primary B cells from cord blood	blood
19	chr13:49141800-49145600	Enhancers	Dnd41	blood
20	chr13:49141800-49145800	Enhancers	Placenta	Placenta
21	chr13:49141800-49146000	Enhancers	Fetal Muscle Leg	muscle
22	chr13:49141800-49150200	Weak transcription	Aorta	Aorta
23	chr13:49142000-49143000	Weak transcription	Brain Anterior Caudate	brain
24	chr13:49142200-49144600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr13:49142200-49145000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr13:49142200-49146000	Enhancers	Spleen	Spleen
27	chr13:49142400-49143000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr13:49142400-49143000	Enhancers	Liver	Liver
29	chr13:49142400-49143000	Enhancers	HSMM	muscle
30	chr13:49142400-49143800	Weak transcription	GM12878-XiMat	blood
31	chr13:49142400-49144000	Enhancers	Psoas Muscle	Psoas
32	chr13:49142400-49144400	Weak transcription	NHDF-Ad	bronchial
33	chr13:49142400-49144600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr13:49142400-49145800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr13:49142400-49148800	Enhancers	Fetal Thymus	thymus
36	chr13:49142600-49143000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr13:49142600-49143200	Enhancers	Colonic Mucosa	Colon
38	chr13:49142600-49143600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr13:49142600-49143800	Enhancers	Colon Smooth Muscle	Colon
40	chr13:49142600-49144200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr13:49142600-49144200	Enhancers	Right Atrium	heart
42	chr13:49142600-49144600	Weak transcription	HMEC	breast
43	chr13:49142600-49145400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr13:49142600-49145400	Enhancers	Esophagus	oesophagus
45	chr13:49142600-49145400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr13:49142600-49145400	Enhancers	HSMMtube	muscle
47	chr13:49142600-49145600	Enhancers	Adipose Nuclei	Adipose
48	chr13:49142600-49145600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr13:49142600-49145600	Enhancers	Stomach Smooth Muscle	stomach
50	chr13:49142800-49143000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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