Variant report

Variant	rs1537724
Chromosome Location	chr9:117931880-117931881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10982541	1.00[CHD][hapmap]
rs12115269	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12115648	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12115782	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12115788	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1414139	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1537723	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1537725	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1537726	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1591420	0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs16932313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4339711	0.85[JPT][hapmap]
rs72760460	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72760463	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72760465	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72760466	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72760467	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72760469	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72762326	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72762328	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72762329	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72762332	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72762335	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72762339	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953140	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][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	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	nsv6681	chr9:117893926-117938609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1537724	PHYHD1	trans	lymphoblastoid	seeQTL
rs1537724	DEC1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117922000-117944600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:117926400-117933600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:117927200-117932200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:117927200-117933000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:117927200-117933000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:117927400-117932000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:117927400-117933000	Weak transcription	A549	lung
8	chr9:117929800-117932200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:117930000-117932000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:117930000-117932600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:117930000-117964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr9:117930200-117932800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:117930200-117932800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr9:117930200-117933000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:117930200-117933000	Weak transcription	NH-A	brain
16	chr9:117930200-117933000	Weak transcription	Osteobl	bone
17	chr9:117930400-117932800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:117930400-117932800	Weak transcription	NHLF	lung
19	chr9:117930600-117932200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:117930600-117932600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:117930600-117932800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:117930600-117932800	Weak transcription	HSMMtube	muscle
23	chr9:117930600-117933000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:117930600-117933000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:117930600-117933000	Weak transcription	HSMM	muscle
26	chr9:117930800-117932600	Weak transcription	HMEC	breast
27	chr9:117930800-117932800	Weak transcription	NHDF-Ad	bronchial
28	chr9:117931400-117932000	Enhancers	Placenta Amnion	Placenta Amnion
29	chr9:117931600-117932800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:117931600-117933400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr9:117931800-117932200	Weak transcription	NHEK	skin
32	chr9:117931800-117933600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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