Variant report

Variant	rs4977569
Chromosome Location	chr9:21894495-21894496
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10117507	0.90[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10811635	0.91[GIH][hapmap];0.87[TSI][hapmap]
rs10965165	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10965168	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10965174	1.00[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10965175	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11526324	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11531660	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11536713	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12236681	0.89[AMR][1000 genomes]
rs12236836	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12238536	0.90[AMR][1000 genomes]
rs12553901	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2027484	0.83[CEU][hapmap]
rs3802394	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4352938	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4587423	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4607709	0.83[CEU][hapmap]
rs4977735	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4977736	0.95[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4977738	0.83[CEU][hapmap]
rs4977742	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4977743	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4977744	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4977745	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56213153	0.88[AMR][1000 genomes]
rs62556506	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62556519	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62556520	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6475592	0.83[CEU][hapmap]
rs7044807	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756641	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7865071	1.00[CEU][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4977569	MTAP	cis	parietal	SCAN
rs4977569	MTAP	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21880400-21901400	Weak transcription	HSMMtube	muscle
2	chr9:21887200-21919000	Weak transcription	Hela-S3	cervix
3	chr9:21888200-21895600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:21890200-21895800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:21890800-21895400	Weak transcription	Placenta	Placenta
6	chr9:21891000-21906000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:21891200-21901800	Weak transcription	HUVEC	blood vessel
8	chr9:21891200-21903600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:21891400-21895200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:21891400-21900800	Weak transcription	Dnd41	blood
11	chr9:21891600-21903000	Weak transcription	Osteobl	bone
12	chr9:21891800-21895200	Weak transcription	Liver	Liver
13	chr9:21891800-21907200	Weak transcription	Left Ventricle	heart
14	chr9:21892200-21894800	Weak transcription	Adipose Nuclei	Adipose
15	chr9:21892200-21903000	Weak transcription	NH-A	brain
16	chr9:21892400-21894800	Weak transcription	HMEC	breast
17	chr9:21892600-21895000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:21892800-21894600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:21892800-21903400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:21893400-21895200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:21893600-21895200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:21893600-21895400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:21893800-21895400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:21894200-21908200	Weak transcription	HSMM	muscle

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