Variant report

Variant	rs7048414
Chromosome Location	chr9:98558844-98558845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98557263..98558873-chr9:98672395..98674331,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10983321	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10988581	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10988792	0.90[TSI][hapmap]
rs10988804	0.90[CEU][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11787559	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11790370	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11790491	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11793298	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11794054	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12001	0.86[GIH][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap]
rs12683634	0.80[ASN][1000 genomes]
rs12685221	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12685807	0.86[GIH][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap]
rs1360064	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16910262	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16910296	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16910298	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16910418	0.90[CEU][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs1831228	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1999023	0.90[CEU][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs2026032	0.80[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2069053	0.90[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2274654	0.83[GIH][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap]
rs34533243	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3780574	0.90[CEU][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs4742775	0.90[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4742781	0.90[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4743372	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4743418	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743436	0.90[CEU][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs73536517	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73656544	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7868270	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv524001	chr9:98556894-98558844	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7048414	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs7048414	LINC00476	cis	Esophagus Mucosa	GTEx
rs7048414	LINC00476	cis	Whole Blood	GTEx
rs7048414	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98548400-98578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:98557400-98563600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr9:98557400-98577200	Weak transcription	Pancreas	Pancrea
4	chr9:98557600-98562600	Weak transcription	HUVEC	blood vessel

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