Variant report

Variant	rs1537733
Chromosome Location	chr9:117983005-117983006
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	chr9:117978231..117979736-chr9:117982363..117984599,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10739433	0.83[CHB][hapmap]
rs10759762	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10817722	0.80[CHB][hapmap]
rs10817728	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1335340	0.83[CHB][hapmap]
rs1335344	0.91[CHB][hapmap]
rs1335345	0.86[CHB][hapmap]
rs1335351	0.91[CHB][hapmap];0.87[MEX][hapmap]
rs1335355	0.86[CHB][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap]
rs1335356	0.86[CHB][hapmap]
rs1335360	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1360823	0.86[CHB][hapmap]
rs1414148	0.86[ASW][hapmap];0.91[CHB][hapmap];0.87[MEX][hapmap];0.81[YRI][hapmap]
rs1414150	0.86[CHB][hapmap]
rs1537734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544126	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4978626	0.91[CHB][hapmap]
rs4979508	0.83[MEX][hapmap]
rs6478147	0.87[CHB][hapmap]
rs6478150	0.87[CHB][hapmap];0.87[MEX][hapmap]
rs6478153	0.91[CHB][hapmap];0.87[MEX][hapmap]
rs7027882	0.86[CHB][hapmap];0.83[MEX][hapmap]
rs7043594	0.87[MEX][hapmap]
rs7043679	0.87[MEX][hapmap]
rs7044001	0.87[MEX][hapmap]
rs7044556	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs945258	0.86[CHB][hapmap]

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	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893769	chr9:117936903-117985886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1537733	PAPPA	cis	cerebellum	SCAN
rs1537733	TNC	cis	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117976600-117985400	Weak transcription	Brain Hippocampus Middle	brain
2	chr9:117976600-117987400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr9:117979800-117984200	Weak transcription	Aorta	Aorta
4	chr9:117980400-117984600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:117980800-117988800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr9:117981400-117983200	Enhancers	Fetal Stomach	stomach
7	chr9:117981400-117988600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:117982000-117983200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:117982000-117983400	Enhancers	Fetal Lung	lung
10	chr9:117982200-117983200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:117982200-117983200	Enhancers	Fetal Muscle Leg	muscle
12	chr9:117982200-117983400	Enhancers	NHEK	skin
13	chr9:117982400-117983200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:117982400-117983200	Enhancers	Fetal Muscle Trunk	muscle
15	chr9:117982400-117983400	Enhancers	Brain Germinal Matrix	brain
16	chr9:117982600-117983200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:117982800-117983200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:117982800-117983200	Enhancers	Fetal Brain Female	brain
19	chr9:117982800-117983200	Enhancers	Fetal Kidney	kidney
20	chr9:117982800-117983400	Enhancers	Adipose Nuclei	Adipose
21	chr9:117982800-117985400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:117983000-117983200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:117983000-117983200	Active TSS	Fetal Brain Male	brain

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