Variant report

Variant	rs6479594
Chromosome Location	chr9:93193062-93193063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10733754	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685168	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs1365368	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2104690	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2114345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2114346	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798041	1.00[JPT][hapmap]
rs4743992	0.86[CHB][hapmap]
rs4744434	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7037348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7865399	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs890427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs890428	0.94[ASN][1000 genomes]
rs981129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs992224	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv482748	chr9:93123377-93279526	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv893565	chr9:93130796-93392332	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv3483705	chr9:93162382-93194535	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3483706	chr9:93162396-93194531	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv614853	chr9:93183404-93266508	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6479594	FAM120A	cis	cerebellum	SCAN
rs6479594	IARS	cis	parietal	SCAN
rs6479594	SPTLC1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93181200-93195200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:93182000-93195000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:93182200-93194800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:93182200-93195000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:93186200-93195200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:93186400-93195000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:93186400-93195200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:93186600-93195200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:93186600-93195400	Weak transcription	Lung	lung
10	chr9:93191400-93195400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:93192000-93195200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:93192400-93193200	Enhancers	A549	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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