Variant report

Variant	rs17109313
Chromosome Location	chr14:79967761-79967762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:79962362..79964375-chr14:79965844..79968447,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10083466	0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10130663	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10133502	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10144362	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10150805	0.96[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10483923	0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1080129	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1080130	0.81[JPT][hapmap]
rs11845632	0.85[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11848580	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11848640	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11849345	0.95[EUR][1000 genomes]
rs11850075	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11850956	0.82[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12588083	1.00[JPT][hapmap]
rs12884436	1.00[JPT][hapmap]
rs12885724	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs17109299	0.81[JPT][hapmap]
rs17763953	0.85[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2043585	0.88[CEU][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2196447	0.82[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2217889	0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2371101	1.00[JPT][hapmap]
rs35879888	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4566079	0.87[TSI][hapmap]
rs4903863	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4903864	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs56111431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61504574	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61995170	0.96[EUR][1000 genomes]
rs61995179	0.90[EUR][1000 genomes]
rs61995180	0.90[EUR][1000 genomes]
rs7145128	0.84[JPT][hapmap]
rs7145991	0.81[JPT][hapmap]
rs7146075	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs7147705	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs7150181	0.92[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7151972	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8017761	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs8020593	0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8021408	0.81[CEU][hapmap]
rs9323673	0.96[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.96[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	nsv902110	chr14:79624492-79998294	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1045241	chr14:79885361-80734201	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1039622	chr14:79908702-80266601	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv902112	chr14:79939393-80050771	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv521160	chr14:79963569-79971835	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv1811223	chr14:79967761-79981954	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17109313	LTBP2	cis	cerebellum	SCAN
rs17109313	C14orf178	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:79966000-79976400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr14:79967000-79967800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr14:79967600-79968800	Weak transcription	Brain Germinal Matrix	brain

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