Variant report

Variant	rs9316399
Chromosome Location	chr13:49116264-49116265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49109335..49111228-chr13:49113801..49116613,2	MCF-7	breast:
2	chr13:49106673..49108535-chr13:49114144..49118573,5	MCF-7	breast:
3	chr13:49109125..49111040-chr13:49114592..49116444,2	K562	blood:
4	chr13:49116019..49118411-chr13:49119146..49122086,2	K562	blood:
5	chr13:49115025..49117372-chr13:49140241..49143183,2	MCF-7	breast:
6	chr13:49113085..49114630-chr13:49116071..49118855,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136161	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11148110	0.81[EUR][1000 genomes]
rs12430215	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.83[YRI][hapmap]
rs12877954	0.83[EUR][1000 genomes]
rs1359688	0.88[EUR][1000 genomes]
rs1536396	0.81[EUR][1000 genomes]
rs1536397	0.83[EUR][1000 genomes]
rs1894255	0.81[CEU][hapmap]
rs1951775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs198563	0.91[CEU][hapmap]
rs198584	0.90[CEU][hapmap]
rs198590	0.91[CEU][hapmap]
rs198607	0.81[CEU][hapmap]
rs198612	0.86[CEU][hapmap]
rs198619	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2104532	0.83[EUR][1000 genomes]
rs2227311	0.82[YRI][hapmap]
rs2406935	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407093	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2407095	0.83[EUR][1000 genomes]
rs2897588	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs399413	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4151450	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4151510	1.00[YRI][hapmap]
rs4635233	0.83[EUR][1000 genomes]
rs520342	0.86[CEU][hapmap]
rs7139578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7329065	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7333360	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7336379	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8002098	0.83[EUR][1000 genomes]
rs9316381	0.90[CEU][hapmap]
rs9316382	0.89[EUR][1000 genomes]
rs9316388	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs9316393	0.83[EUR][1000 genomes]
rs9316394	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9316395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs943278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs943280	0.85[EUR][1000 genomes]
rs943283	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526475	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9526479	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526481	0.83[EUR][1000 genomes]
rs9526483	0.81[EUR][1000 genomes]
rs9535032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9535033	0.81[EUR][1000 genomes]
rs9535035	0.89[EUR][1000 genomes]
rs9535038	0.83[EUR][1000 genomes]
rs9535042	0.82[EUR][1000 genomes]
rs9535043	0.80[EUR][1000 genomes]
rs9535045	0.83[EUR][1000 genomes]
rs9535046	0.83[EUR][1000 genomes]
rs9562819	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs9568043	0.88[EUR][1000 genomes]
rs9568047	0.86[EUR][1000 genomes]
rs9568049	0.83[EUR][1000 genomes]
rs9568050	0.83[EUR][1000 genomes]
rs9634680	0.83[EUR][1000 genomes]
rs990814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9316399	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49107800-49116400	Weak transcription	Lung	lung
2	chr13:49107800-49116800	Weak transcription	Pancreas	Pancrea
3	chr13:49108000-49116600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr13:49108400-49116400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr13:49110800-49116400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr13:49111200-49116600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr13:49114000-49116600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:49114200-49116400	Weak transcription	Adipose Nuclei	Adipose
9	chr13:49114200-49116400	Weak transcription	Esophagus	oesophagus
10	chr13:49115800-49118400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr13:49115800-49118400	Enhancers	Fetal Heart	heart
12	chr13:49116000-49116600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr13:49116000-49116800	Enhancers	Dnd41	blood
14	chr13:49116000-49117400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr13:49116200-49116400	Enhancers	Brain Substantia Nigra	brain
16	chr13:49116200-49116400	Enhancers	HepG2	liver
17	chr13:49116200-49116600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr13:49116200-49116600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr13:49116200-49116800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:49116200-49116800	Enhancers	Brain Hippocampus Middle	brain
21	chr13:49116200-49116800	Enhancers	Ovary	ovary
22	chr13:49116200-49116800	Enhancers	Right Atrium	heart
23	chr13:49116200-49116800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr13:49116200-49116800	Enhancers	Stomach Smooth Muscle	stomach
25	chr13:49116200-49116800	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr13:49116200-49117000	Enhancers	Right Ventricle	heart
27	chr13:49116200-49117200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr13:49116200-49117200	Enhancers	Fetal Muscle Trunk	muscle
29	chr13:49116200-49117200	Enhancers	Fetal Stomach	stomach
30	chr13:49116200-49117200	Enhancers	Fetal Thymus	thymus
31	chr13:49116200-49117200	Enhancers	Left Ventricle	heart
32	chr13:49116200-49117400	Enhancers	Fetal Muscle Leg	muscle
33	chr13:49116200-49117400	Enhancers	Psoas Muscle	Psoas
34	chr13:49116200-49117600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr13:49116200-49117600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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