Variant report

Variant	rs9535006
Chromosome Location	chr13:48849803-48849804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48839695..48841819-chr13:48848879..48850902,2	MCF-7	breast:
2	chr13:48848862..48851503-chr13:48870489..48872026,2	K562	blood:
3	chr13:48848433..48850155-chr13:48876648..48878304,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139687	Chromatin interaction
ENSG00000231473	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10219833	0.87[EUR][1000 genomes]
rs12100135	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12583516	0.88[ASN][1000 genomes]
rs12871662	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12871740	0.86[EUR][1000 genomes]
rs12875750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1573601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1886795	0.87[EUR][1000 genomes]
rs1894255	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs1925744	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1925745	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1951775	0.84[CEU][hapmap]
rs1981434	0.90[CEU][hapmap]
rs198561	0.83[EUR][1000 genomes]
rs198563	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198584	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs198590	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198604	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs198607	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap]
rs198612	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198619	0.90[CEU][hapmap]
rs198634	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2243461	0.86[EUR][1000 genomes]
rs2243626	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2248488	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs2251813	0.86[EUR][1000 genomes]
rs2253520	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254423	0.86[EUR][1000 genomes]
rs2406933	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2854345	0.94[ASN][1000 genomes]
rs2854355	0.86[EUR][1000 genomes]
rs34217484	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs375105	0.81[EUR][1000 genomes]
rs3803188	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3809328	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3818455	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4151450	0.90[CEU][hapmap]
rs4151520	0.87[ASN][1000 genomes]
rs4594153	0.84[EUR][1000 genomes]
rs4600372	0.81[EUR][1000 genomes]
rs520342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61973349	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9316369	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]
rs9526465	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs9526466	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526470	0.89[EUR][1000 genomes]
rs9534998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535000	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535002	0.86[EUR][1000 genomes]
rs9535003	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535007	0.84[EUR][1000 genomes]
rs9535009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535011	0.87[EUR][1000 genomes]
rs9535032	0.85[CEU][hapmap]
rs9562815	0.85[ASN][1000 genomes]
rs9568025	0.88[ASN][1000 genomes]
rs9568026	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568027	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568028	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568029	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9568032	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568033	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568034	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568035	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.95[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9535006	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs9535006	LPAR6	cis	parietal	SCAN
rs9535006	ATAD2	trans	parietal	SCAN
rs9535006	C13orf1	cis	cerebellum	SCAN
rs9535006	ITM2B	cis	lymphoblastoid	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48833800-48851600	Weak transcription	Fetal Heart	heart
2	chr13:48837800-48853000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:48837800-48856400	Weak transcription	Colon Smooth Muscle	Colon
4	chr13:48838000-48850000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:48838000-48850000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr13:48838000-48852800	Weak transcription	HUVEC	blood vessel
7	chr13:48839800-48850200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:48840000-48851600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:48841800-48852000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr13:48841800-48853200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:48843800-48850400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr13:48844000-48850600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr13:48844200-48850000	Weak transcription	HSMM	muscle
14	chr13:48844200-48850600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr13:48844200-48853000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr13:48844400-48850000	Weak transcription	Left Ventricle	heart
17	chr13:48844400-48850200	Weak transcription	Fetal Stomach	stomach
18	chr13:48844400-48850200	Weak transcription	Ovary	ovary
19	chr13:48844400-48851400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr13:48844400-48851600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr13:48844400-48853000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr13:48844400-48853000	Weak transcription	Brain Anterior Caudate	brain
23	chr13:48844400-48853000	Weak transcription	Fetal Muscle Leg	muscle
24	chr13:48844400-48857600	Weak transcription	HSMMtube	muscle
25	chr13:48844400-48877200	Weak transcription	Aorta	Aorta
26	chr13:48845200-48850400	Weak transcription	Fetal Thymus	thymus
27	chr13:48846200-48851200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr13:48847800-48853000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:48848000-48853000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr13:48848000-48853000	Weak transcription	Brain Hippocampus Middle	brain
31	chr13:48848000-48853000	Weak transcription	Brain Substantia Nigra	brain
32	chr13:48849600-48850200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:48849800-48850200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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