Variant report

Variant	rs12340196
Chromosome Location	chr9:21399121-21399122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr9:21399097-21399461	HepG2	liver:	n/a	chr9:21399315-21399326 chr9:21399186-21399197 chr9:21399179-21399193 chr9:21399186-21399197 chr9:21399185-21399196 chr9:21399176-21399196 chr9:21399306-21399323 chr9:21399178-21399194 chr9:21399185-21399196

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IFNA2-2	chr9:21398613-21399138	NONHSAT130382

Variant related genes	Relation type
ENSG00000261696	TF binding region
IFNA12P	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10114175	0.81[EUR][1000 genomes]
rs10114286	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10121687	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10125532	0.80[EUR][1000 genomes]
rs11999696	0.84[EUR][1000 genomes]
rs12336789	0.81[EUR][1000 genomes]
rs12340718	0.81[EUR][1000 genomes]
rs1330321	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17334047	0.81[EUR][1000 genomes]
rs28383780	0.84[EUR][1000 genomes]
rs28383791	0.97[EUR][1000 genomes]
rs28383792	0.97[EUR][1000 genomes]
rs35000944	0.84[EUR][1000 genomes]
rs35101870	0.81[EUR][1000 genomes]
rs35353365	0.81[EUR][1000 genomes]
rs72695797	1.00[AMR][1000 genomes]
rs72697321	0.81[EUR][1000 genomes]
rs72697322	0.81[EUR][1000 genomes]
rs72697324	0.81[EUR][1000 genomes]
rs72697326	0.81[EUR][1000 genomes]
rs72697327	0.81[EUR][1000 genomes]
rs72699197	0.81[EUR][1000 genomes]
rs72699198	0.81[EUR][1000 genomes]
rs72699199	0.81[EUR][1000 genomes]
rs72699200	0.81[EUR][1000 genomes]
rs72699201	0.81[EUR][1000 genomes]
rs72699202	0.81[EUR][1000 genomes]
rs72701303	0.81[EUR][1000 genomes]
rs72701305	0.81[EUR][1000 genomes]
rs72701306	0.81[EUR][1000 genomes]
rs72701307	0.81[EUR][1000 genomes]
rs72701308	0.81[EUR][1000 genomes]
rs72701309	0.81[EUR][1000 genomes]
rs72701311	0.81[EUR][1000 genomes]
rs72701312	0.81[EUR][1000 genomes]
rs72701313	0.81[EUR][1000 genomes]
rs72701314	0.81[EUR][1000 genomes]
rs72701315	0.81[EUR][1000 genomes]
rs72701316	0.81[EUR][1000 genomes]
rs72701317	0.81[EUR][1000 genomes]
rs72701318	0.81[EUR][1000 genomes]
rs72701319	0.81[EUR][1000 genomes]
rs72701320	0.81[EUR][1000 genomes]
rs72701321	0.84[EUR][1000 genomes]
rs72701344	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72701345	1.00[EUR][1000 genomes]
rs72701348	0.95[EUR][1000 genomes]
rs72701355	0.97[EUR][1000 genomes]
rs72701357	0.97[EUR][1000 genomes]
rs72701366	0.80[EUR][1000 genomes]
rs72701368	0.80[EUR][1000 genomes]
rs7862030	0.81[EUR][1000 genomes]
rs7865334	1.00[AMR][1000 genomes]
rs9333356	0.81[EUR][1000 genomes]

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	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
2	nsv892737	chr9:21352862-21408824	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2752289	chr9:21361957-21499624	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv892738	chr9:21371264-21413085	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv466297	chr9:21391698-21507589	Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv613758	chr9:21391698-21507589	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21396600-21399800	Weak transcription	GM12878-XiMat	blood
2	chr9:21396600-21401800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:21396600-21402200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:21396600-21402200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:21399000-21399200	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:21399000-21402000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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