Variant report

Variant	rs1537016
Chromosome Location	chr9:117882387-117882388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10125663	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10817713	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982553	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335332	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414137	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1537015	0.87[CEU][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1537720	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071520	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4979496	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7853883	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884290	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945256	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs945257	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1537016	COL27A1	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117881000-117882600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:117881200-117882400	Weak transcription	Lung	lung
3	chr9:117881200-117882600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:117881200-117883200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:117881200-117884000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:117881400-117883200	Weak transcription	Brain Germinal Matrix	brain
7	chr9:117881400-117883200	Weak transcription	Esophagus	oesophagus
8	chr9:117881400-117884400	Enhancers	NH-A	brain
9	chr9:117881400-117886000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr9:117881600-117882400	Enhancers	Fetal Kidney	kidney
11	chr9:117881600-117882800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:117881600-117882800	Weak transcription	Fetal Lung	lung
13	chr9:117881600-117883200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:117881600-117883200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:117881600-117883200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:117881600-117884200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:117881600-117884200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:117881600-117884400	Enhancers	NHEK	skin
19	chr9:117881800-117882800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:117881800-117883200	Weak transcription	HMEC	breast
21	chr9:117881800-117883600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:117881800-117883800	Weak transcription	HSMM	muscle
23	chr9:117881800-117884000	Enhancers	Colon Smooth Muscle	Colon
24	chr9:117881800-117884000	Enhancers	Stomach Smooth Muscle	stomach
25	chr9:117881800-117884400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr9:117882000-117882400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:117882000-117888800	Weak transcription	NHLF	lung
28	chr9:117882200-117883200	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:117882200-117883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:117882200-117883400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:117882200-117883800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:117882200-117883800	Weak transcription	Osteobl	bone

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