Variant report

Variant	rs1536423
Chromosome Location	chr9:95323669-95323670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10115937	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10120210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10120292	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10125510	1.00[YRI][hapmap]
rs10435919	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10761159	1.00[YRI][hapmap]
rs10992439	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs1111047	0.96[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2007245	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2131918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2296668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2761680	1.00[YRI][hapmap]
rs4744142	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6479421	1.00[YRI][hapmap]
rs6479424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479427	0.96[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6479429	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs7043114	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7864453	1.00[YRI][hapmap]
rs7864757	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7873646	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs912260	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs944949	1.00[YRI][hapmap]
rs9886781	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9969804	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1052846	chr9:95291909-95366109	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1536423	CENPP	cis	cerebellum	SCAN
rs1536423	CENPP	cis	parietal	SCAN
rs1536423	IPPK	cis	cerebellum	SCAN
rs1536423	ZNF484	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95308600-95324000	Weak transcription	Fetal Intestine Small	intestine
2	chr9:95320600-95324200	Weak transcription	Small Intestine	intestine
3	chr9:95321200-95325400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:95321400-95324000	Weak transcription	Esophagus	oesophagus
5	chr9:95321600-95325400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr9:95321800-95326400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:95322000-95324200	Weak transcription	Adipose Nuclei	Adipose
8	chr9:95323200-95324800	Weak transcription	Psoas Muscle	Psoas
9	chr9:95323400-95324200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:95323400-95324200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr9:95323400-95324400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:95323400-95324400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:95323400-95324400	Enhancers	HMEC	breast
14	chr9:95323400-95324400	Enhancers	NHEK	skin
15	chr9:95323400-95325200	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr9:95323400-95325600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:95323400-95325800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr9:95323400-95326600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:95323400-95327800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:95323600-95323800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr9:95323600-95323800	Enhancers	Fetal Kidney	kidney
22	chr9:95323600-95324400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:95323600-95325400	Weak transcription	HSMMtube	muscle
24	chr9:95323600-95326000	Enhancers	NHLF	lung
25	chr9:95323600-95326400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr9:95323600-95326400	Enhancers	NH-A	brain
27	chr9:95323600-95327800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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