Variant report

Variant	rs16932313
Chromosome Location	chr9:117933506-117933507
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10759758	0.83[LWK][hapmap]
rs10982541	1.00[CHD][hapmap]
rs12115269	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12115648	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12115782	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12115788	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12348952	0.80[YRI][hapmap]
rs1414139	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1537723	1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1537724	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]
rs1537725	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1537726	1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[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]
rs4339711	0.85[JPT][hapmap]
rs72760460	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72760463	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72760465	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72760466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72760467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72760469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72762326	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72762328	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72762329	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72762332	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72762335	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72762339	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953140	1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.93[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
rs16932313	PHYHD1	trans	lymphoblastoid	seeQTL
rs16932313	DEC1	cis	Nerve Tibial	GTEx

Chromatin state (count:31 , 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	chr9:117930000-117964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:117931800-117933600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr9:117932000-117933600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr9:117932000-117933600	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr9:117932000-117935200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:117932200-117933600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr9:117932200-117933600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr9:117932200-117933600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:117932200-117933600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:117932200-117933600	Enhancers	NHEK	skin
13	chr9:117932200-117934000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr9:117932400-117934800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:117932600-117933800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:117932600-117933800	Enhancers	HMEC	breast
17	chr9:117932800-117933600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:117932800-117933600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:117932800-117933600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:117932800-117933600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr9:117932800-117933600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:117932800-117933600	Enhancers	Fetal Intestine Small	intestine
23	chr9:117932800-117933600	Enhancers	HSMMtube	muscle
24	chr9:117932800-117933600	Enhancers	NHDF-Ad	bronchial
25	chr9:117932800-117933600	Enhancers	NHLF	lung
26	chr9:117933000-117933600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:117933000-117933600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:117933400-117933600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:117933400-117941400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:117933400-117942200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:117933400-117943400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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