Variant report

Variant	rs9526465
Chromosome Location	chr13:48824231-48824232
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr13:48824157-48824268	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:48823943..48826005-chr13:48829324..48832126,2	MCF-7	breast:
2	chr13:48808662..48812732-chr13:48820679..48824988,4	K562	blood:
3	chr13:48818594..48820603-chr13:48823008..48825068,2	K562	blood:
4	chr13:48823136..48824828-chr13:48830580..48833314,2	K562	blood:
5	chr13:48821859..48823433-chr13:48823611..48826198,2	K562	blood:
6	chr13:48814554..48816735-chr13:48821665..48824579,2	MCF-7	breast:

No data

Variant related genes	Relation type
ITM2B	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10219833	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12100135	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs12430215	0.91[CEU][hapmap]
rs12871662	0.92[EUR][1000 genomes]
rs12871740	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12875750	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1573601	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs1886795	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925744	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1925745	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1951775	0.95[CEU][hapmap]
rs1981434	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs198563	0.86[CEU][hapmap]
rs198604	0.81[CEU][hapmap]
rs198607	0.85[CEU][hapmap]
rs198612	0.82[CEU][hapmap]
rs198619	1.00[CEU][hapmap]
rs2243461	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243626	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248488	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2251813	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253520	0.84[EUR][1000 genomes]
rs2254423	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2406933	0.84[EUR][1000 genomes]
rs2854355	0.81[EUR][1000 genomes]
rs34217484	0.85[EUR][1000 genomes]
rs3803188	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3809328	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs3818455	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs399413	0.90[CEU][hapmap]
rs4151450	1.00[CEU][hapmap]
rs4594153	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4600372	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs520342	0.90[CEU][hapmap]
rs61973349	0.92[EUR][1000 genomes]
rs7322987	0.89[ASN][1000 genomes]
rs7358982	0.85[EUR][1000 genomes]
rs7984554	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7984795	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7999447	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8001315	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316367	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs9316369	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs9526466	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9526470	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9526475	0.90[CEU][hapmap]
rs9534996	0.89[ASN][1000 genomes]
rs9534998	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs9535000	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9535002	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535003	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9535006	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs9535007	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535009	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs9535011	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535032	0.95[CEU][hapmap]
rs9562819	0.86[CEU][hapmap]
rs9568026	0.82[EUR][1000 genomes]
rs9568027	0.92[EUR][1000 genomes]
rs9568028	0.92[EUR][1000 genomes]
rs9568029	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568035	0.81[CEU][hapmap]

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	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	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
rs9526465	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48808400-48829000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:48808400-48829200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:48808400-48843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:48809600-48837400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr13:48809800-48829200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:48810400-48830200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr13:48810800-48841000	Weak transcription	Hela-S3	cervix
8	chr13:48811200-48843800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr13:48811400-48828200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:48811600-48825800	Weak transcription	Gastric	stomach
11	chr13:48811600-48827600	Weak transcription	Thymus	Thymus
12	chr13:48811600-48829000	Weak transcription	Colonic Mucosa	Colon
13	chr13:48811600-48829600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr13:48811600-48835600	Weak transcription	Fetal Brain Male	brain
15	chr13:48811600-48836800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr13:48811800-48825200	Weak transcription	Fetal Brain Female	brain
17	chr13:48811800-48826400	Weak transcription	Psoas Muscle	Psoas
18	chr13:48811800-48827600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:48811800-48828000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr13:48811800-48828200	Weak transcription	Aorta	Aorta
21	chr13:48812000-48825000	Weak transcription	Brain Substantia Nigra	brain
22	chr13:48812200-48825000	Weak transcription	Brain Angular Gyrus	brain
23	chr13:48812200-48825200	Weak transcription	Fetal Kidney	kidney
24	chr13:48812200-48825200	Weak transcription	HSMMtube	muscle
25	chr13:48812200-48826200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr13:48812200-48828200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr13:48812400-48826200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr13:48812400-48827600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr13:48812400-48827600	Weak transcription	HUVEC	blood vessel
30	chr13:48812400-48827800	Weak transcription	HMEC	breast
31	chr13:48812400-48827800	Weak transcription	NH-A	brain
32	chr13:48812400-48828000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr13:48812400-48828200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr13:48812600-48827800	Weak transcription	Osteobl	bone
35	chr13:48813400-48829600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr13:48813600-48826400	Weak transcription	Right Atrium	heart
37	chr13:48813600-48828200	Weak transcription	HSMM	muscle
38	chr13:48813800-48825800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr13:48814000-48826000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr13:48814000-48828200	Weak transcription	NHEK	skin
41	chr13:48814200-48827600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr13:48814200-48827800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr13:48814200-48827800	Weak transcription	A549	lung
44	chr13:48814200-48828000	Weak transcription	Fetal Intestine Large	intestine
45	chr13:48814200-48828200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr13:48814600-48826400	Weak transcription	Fetal Stomach	stomach
47	chr13:48814600-48827800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr13:48815200-48827800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr13:48815400-48825000	Weak transcription	Fetal Muscle Leg	muscle
50	chr13:48815600-48824400	Weak transcription	Left Ventricle	heart

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