Variant report

Variant	rs9292201
Chromosome Location	chr5:58582613-58582614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10036406	0.81[CEU][hapmap]
rs10038599	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs10055446	0.80[CEU][hapmap]
rs10059709	0.82[GIH][hapmap]
rs10060200	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs10061786	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs10070294	0.84[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs10075364	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10079396	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs13328160	0.91[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13328175	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13328226	0.91[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13354210	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17444059	0.84[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs17528473	0.91[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17528634	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17724250	0.90[CEU][hapmap]
rs17780213	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17780584	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs17780740	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs17780836	1.00[JPT][hapmap]
rs1824159	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs2044419	1.00[ASN][1000 genomes]
rs2112959	0.82[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2194210	0.88[CEU][hapmap]
rs28529077	0.88[EUR][1000 genomes]
rs56183128	1.00[ASN][1000 genomes]
rs57516309	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61683381	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881054	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72765953	0.88[EUR][1000 genomes]
rs72765961	0.88[EUR][1000 genomes]
rs72765990	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765993	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767710	1.00[ASN][1000 genomes]
rs9686434	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9292201	SLC38A9	cis	parietal	SCAN
rs9292201	PHYHIP	trans	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58572000-58582800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:58572200-58583000	Weak transcription	Left Ventricle	heart
3	chr5:58573400-58583400	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:58573600-58582800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:58573600-58583000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:58573600-58583000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:58574200-58590200	Weak transcription	Right Atrium	heart
8	chr5:58574800-58582800	Weak transcription	Psoas Muscle	Psoas
9	chr5:58581400-58583200	Enhancers	A549	lung
10	chr5:58581800-58583000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:58582000-58582800	Weak transcription	Hela-S3	cervix
12	chr5:58582000-58582800	Weak transcription	HUVEC	blood vessel
13	chr5:58582400-58587000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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