Variant report

Variant	rs9316369
Chromosome Location	chr13:48817074-48817075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48816853..48818808-chr13:48829859..48831555,2	K562	blood:
2	chr13:48813965..48816179-chr13:48816812..48818519,2	MCF-7	breast:
3	chr13:48816672..48819257-chr13:48820159..48822647,2	K562	blood:
4	chr13:48805640..48809196-chr13:48816865..48821850,5	MCF-7	breast:
5	chr13:48610565..48612356-chr13:48816813..48819591,2	K562	blood:

Variant related genes	Relation type
ENSG00000136143	Chromatin interaction
ENSG00000136159	Chromatin interaction
ENSG00000136156	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10219833	0.87[EUR][1000 genomes]
rs12100135	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12430215	0.80[CEU][hapmap]
rs12583516	0.84[ASN][1000 genomes]
rs12871662	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12871740	0.86[EUR][1000 genomes]
rs12875750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1886795	0.87[EUR][1000 genomes]
rs1894255	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1925744	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925745	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951775	0.85[CEU][hapmap]
rs1981434	0.91[CEU][hapmap]
rs198561	0.83[EUR][1000 genomes]
rs198563	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs198604	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs198607	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198612	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs198619	0.91[CEU][hapmap]
rs198634	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2243461	0.86[EUR][1000 genomes]
rs2243626	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2248488	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2251813	0.86[EUR][1000 genomes]
rs2253520	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2254423	0.86[EUR][1000 genomes]
rs2406933	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2854345	0.91[ASN][1000 genomes]
rs2854355	0.86[EUR][1000 genomes]
rs34217484	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs375105	0.81[EUR][1000 genomes]
rs3803188	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809328	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818455	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4151450	0.90[CEU][hapmap]
rs4151520	0.84[ASN][1000 genomes]
rs4594153	0.84[EUR][1000 genomes]
rs4600372	0.81[EUR][1000 genomes]
rs520342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61973349	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7358982	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7984554	0.86[EUR][1000 genomes]
rs7984795	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs7999447	0.87[EUR][1000 genomes]
rs8001315	0.86[EUR][1000 genomes]
rs9316367	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526465	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs9526466	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526470	0.89[EUR][1000 genomes]
rs9534998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535000	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535002	0.86[EUR][1000 genomes]
rs9535003	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535007	0.84[EUR][1000 genomes]
rs9535009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535011	0.87[EUR][1000 genomes]
rs9535032	0.85[CEU][hapmap]
rs9562815	0.82[ASN][1000 genomes]
rs9568025	0.92[ASN][1000 genomes]
rs9568026	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568027	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568028	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568029	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9568032	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568033	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568034	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568035	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.92[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	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
rs9316369	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 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	chr13:48811200-48819200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr13:48811200-48843800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr13:48811400-48828200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:48811600-48819800	Weak transcription	Spleen	Spleen
12	chr13:48811600-48825800	Weak transcription	Gastric	stomach
13	chr13:48811600-48827600	Weak transcription	Thymus	Thymus
14	chr13:48811600-48829000	Weak transcription	Colonic Mucosa	Colon
15	chr13:48811600-48829600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr13:48811600-48835600	Weak transcription	Fetal Brain Male	brain
17	chr13:48811600-48836800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr13:48811800-48818200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr13:48811800-48825200	Weak transcription	Fetal Brain Female	brain
20	chr13:48811800-48826400	Weak transcription	Psoas Muscle	Psoas
21	chr13:48811800-48827600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr13:48811800-48828000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr13:48811800-48828200	Weak transcription	Aorta	Aorta
24	chr13:48812000-48825000	Weak transcription	Brain Substantia Nigra	brain
25	chr13:48812200-48819200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr13:48812200-48825000	Weak transcription	Brain Angular Gyrus	brain
27	chr13:48812200-48825200	Weak transcription	Fetal Kidney	kidney
28	chr13:48812200-48825200	Weak transcription	HSMMtube	muscle
29	chr13:48812200-48826200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr13:48812200-48828200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr13:48812400-48818600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
32	chr13:48812400-48819800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr13:48812400-48823000	Weak transcription	Fetal Lung	lung
34	chr13:48812400-48826200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:48812400-48827600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:48812400-48827600	Weak transcription	HUVEC	blood vessel
37	chr13:48812400-48827800	Weak transcription	HMEC	breast
38	chr13:48812400-48827800	Weak transcription	NH-A	brain
39	chr13:48812400-48828000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr13:48812400-48828200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr13:48812600-48827800	Weak transcription	Osteobl	bone
42	chr13:48813200-48818600	Strong transcription	Fetal Thymus	thymus
43	chr13:48813400-48829600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr13:48813600-48818400	Strong transcription	Dnd41	blood
45	chr13:48813600-48826400	Weak transcription	Right Atrium	heart
46	chr13:48813600-48828200	Weak transcription	HSMM	muscle
47	chr13:48813800-48817600	Weak transcription	Pancreas	Pancrea
48	chr13:48813800-48818600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr13:48813800-48825800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:48814000-48817400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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