Variant report

Variant	rs9526816
Chromosome Location	chr13:52555288-52555289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52538063..52541078-chr13:52554449..52557060,3	K562	blood:
2	chr13:52546299..52549465-chr13:52553764..52557298,3	K562	blood:
3	chr13:52549808..52551859-chr13:52553072..52555669,2	K562	blood:
4	chr13:52538417..52541078-chr13:52553924..52556751,2	K562	blood:

Variant related genes	Relation type
ENSG00000236044	Chromatin interaction
ENSG00000123191	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2094354	0.88[EUR][1000 genomes]
rs2147362	0.88[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs4941716	0.88[CEU][hapmap]
rs7328090	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7336985	1.00[ASW][hapmap]
rs9316568	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv455888	chr13:52491193-52570728	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv561649	chr13:52491193-52570728	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1041996	chr13:52544805-52581501	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
8	esv2763022	chr13:52544978-52581513	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
9	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	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
rs9526816	LOC440138	cis	multi-tissue	Pritchard

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
3	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr13:52530200-52555400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr13:52534400-52555400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:52544800-52556600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:52545000-52555400	Weak transcription	Adipose Nuclei	Adipose
8	chr13:52545000-52555600	Weak transcription	Aorta	Aorta
9	chr13:52545400-52555400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:52549000-52555400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr13:52549000-52555600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr13:52551600-52555800	Enhancers	Fetal Intestine Small	intestine
13	chr13:52552600-52555800	Enhancers	Stomach Mucosa	stomach
14	chr13:52553000-52555800	Enhancers	Fetal Lung	lung
15	chr13:52553200-52556800	Enhancers	HepG2	liver
16	chr13:52553400-52555400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:52553400-52555400	Weak transcription	Left Ventricle	heart
18	chr13:52553400-52555400	Weak transcription	Ovary	ovary
19	chr13:52553400-52555400	Weak transcription	Psoas Muscle	Psoas
20	chr13:52553400-52555400	Weak transcription	Right Atrium	heart
21	chr13:52553400-52556800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr13:52553400-52556800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr13:52553400-52569400	Weak transcription	Pancreas	Pancrea
24	chr13:52553600-52555800	Enhancers	K562	blood
25	chr13:52554200-52556400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr13:52554400-52555400	Weak transcription	Fetal Intestine Large	intestine
27	chr13:52554600-52555600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr13:52554800-52556000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr13:52554800-52556000	Flanking Active TSS	Fetal Heart	heart
30	chr13:52554800-52556400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr13:52555000-52555400	Active TSS	Right Ventricle	heart
32	chr13:52555000-52555400	Active TSS	HSMMtube	muscle
33	chr13:52555000-52555400	Enhancers	Osteobl	bone
34	chr13:52555000-52555800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr13:52555200-52555800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr13:52555200-52556200	Enhancers	Placenta	Placenta

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