Variant report

Variant	rs11070396
Chromosome Location	chr15:43522922-43522923
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43520201..43525813-chr15:43528150..43534434,7	K562	blood:

Variant related genes	Relation type
ENSG00000104055	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11070391	0.89[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs11070397	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070398	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11855754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592725	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12899266	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1462856	0.89[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs16957511	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834643	0.92[EUR][1000 genomes]
rs2042742	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2241516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412752	0.82[JPT][hapmap]
rs28585036	0.86[CEU][hapmap]
rs28756768	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2899077	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2947019	0.84[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34646108	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784267	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784268	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924704	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs4924709	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs494863	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs495286	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs497138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs499280	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530305	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs531850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs538218	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs540587	0.88[CEU][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6493077	0.89[CEU][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs6493078	0.86[ASN][1000 genomes]
rs7174915	0.89[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs7183814	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8027371	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[ASN][1000 genomes]
rs9652444	0.84[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11070396	TGM5	cis	lymphoblastoid	seeQTL
rs11070396	CCNDBP1	cis	Lymphoblastoid	GTEx
rs11070396	C15orf63	cis	lymphoblastoid	seeQTL
rs11070396	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs11070396	CCNDBP1	cis	multi-tissue	Pritchard
rs11070396	ELL3	cis	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43511800-43526600	Weak transcription	Esophagus	oesophagus
2	chr15:43521400-43523000	Enhancers	Brain Cingulate Gyrus	brain
3	chr15:43521400-43523200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr15:43521600-43523000	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr15:43521600-43523200	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr15:43521600-43523400	Enhancers	Brain Hippocampus Middle	brain
7	chr15:43521600-43523800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:43521600-43525600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:43521800-43523200	Enhancers	Brain Substantia Nigra	brain
10	chr15:43521800-43523400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:43521800-43523400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:43521800-43523600	Enhancers	Adipose Nuclei	Adipose
13	chr15:43522200-43523000	Enhancers	Brain Anterior Caudate	brain
14	chr15:43522400-43523400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr15:43522400-43523600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:43522400-43526000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr15:43522600-43523200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr15:43522600-43523200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:43522600-43523400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr15:43522600-43523400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:43522600-43523400	Flanking Active TSS	K562	blood
22	chr15:43522800-43523400	Enhancers	Lung	lung

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