Variant report

Variant	rs10992087
Chromosome Location	chr9:94533121-94533122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94530728..94533133-chr9:94548212..94550355,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10512217	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10820902	0.81[YRI][hapmap]
rs10992086	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992088	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992089	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12235606	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12235611	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12237459	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12238428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12685213	0.92[MKK][hapmap]
rs12685849	0.84[MKK][hapmap]
rs16907741	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16907754	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16907761	0.87[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];0.87[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16907764	1.00[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];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16907776	0.81[MKK][hapmap]
rs17586213	0.84[GIH][hapmap]
rs34854279	0.99[ASN][1000 genomes]
rs3802377	0.81[MKK][hapmap]
rs3802378	0.81[MKK][hapmap]
rs3802379	0.84[GIH][hapmap]
rs4452868	0.92[MKK][hapmap]
rs4467997	0.85[JPT][hapmap]
rs4595186	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744097	0.85[JPT][hapmap]
rs60099576	0.99[ASN][1000 genomes]
rs7026175	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7039620	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs73511102	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7855079	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv6612	chr9:94490644-94535738	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1036176	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv540171	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10992087	PNLDC1	trans	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94487000-94535400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:94527200-94533200	Weak transcription	Fetal Intestine Large	intestine
3	chr9:94527600-94538800	Weak transcription	K562	blood
4	chr9:94528600-94533200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr9:94529400-94539800	Enhancers	Colon Smooth Muscle	Colon
6	chr9:94530400-94535200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:94531600-94533600	Enhancers	Esophagus	oesophagus
8	chr9:94532200-94533200	Enhancers	Rectal Smooth Muscle	rectum
9	chr9:94532200-94537000	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr9:94532200-94539200	Enhancers	Fetal Heart	heart
11	chr9:94532400-94533400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:94532400-94533600	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr9:94532400-94534600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:94532600-94533200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:94532600-94533200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:94532600-94533200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:94532600-94533200	Enhancers	Duodenum Mucosa	Duodenum
18	chr9:94532600-94533400	Enhancers	Fetal Brain Male	brain
19	chr9:94532600-94533400	Enhancers	Fetal Thymus	thymus
20	chr9:94532600-94533600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:94532600-94533600	Enhancers	Placenta	Placenta
22	chr9:94532600-94534000	Enhancers	HMEC	breast
23	chr9:94532600-94534400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr9:94532800-94533200	Enhancers	NHLF	lung
25	chr9:94532800-94533200	Enhancers	Osteobl	bone
26	chr9:94532800-94533400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr9:94532800-94533400	Enhancers	Colonic Mucosa	Colon
28	chr9:94532800-94533600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr9:94532800-94533800	Flanking Active TSS	NHEK	skin
30	chr9:94532800-94534000	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr9:94532800-94534000	Enhancers	Stomach Mucosa	stomach
32	chr9:94532800-94534200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr9:94532800-94534400	Enhancers	HSMM	muscle
34	chr9:94532800-94534800	Enhancers	Ovary	ovary
35	chr9:94532800-94535400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:94532800-94536000	Enhancers	HSMMtube	muscle
37	chr9:94532800-94536400	Enhancers	Fetal Lung	lung
38	chr9:94533000-94533200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr9:94533000-94533400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:94533000-94533400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:94533000-94533400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:94533000-94533400	Enhancers	Adipose Nuclei	Adipose
43	chr9:94533000-94533400	Enhancers	Gastric	stomach
44	chr9:94533000-94533400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr9:94533000-94533400	Flanking Active TSS	NHDF-Ad	bronchial
46	chr9:94533000-94533800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:94533000-94533800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr9:94533000-94534200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:94533000-94534200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:94533000-94534200	Enhancers	Muscle Satellite Cultured Cells	--

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