Variant report

Variant	rs1990035
Chromosome Location	chr14:71695958-71695959
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10130213	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158898	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs11844320	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11850267	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11851589	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109116	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177822	0.83[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17178206	1.00[YRI][hapmap]
rs17767266	0.94[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767296	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767392	1.00[YRI][hapmap]
rs17767410	1.00[YRI][hapmap]
rs2108707	1.00[YRI][hapmap]
rs2877729	1.00[YRI][hapmap]
rs34674149	1.00[YRI][hapmap]
rs4899390	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902916	0.83[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902917	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902918	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902922	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55737377	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59985720	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60526802	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60536344	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61174376	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989206	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989207	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989208	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574006	0.83[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574007	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146169	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7150921	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153194	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156194	0.93[MEX][hapmap]
rs723966	1.00[YRI][hapmap]
rs725673	1.00[YRI][hapmap]
rs72726657	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72726677	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005089	0.83[CEU][hapmap]
rs8005615	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005925	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8007068	1.00[YRI][hapmap]
rs8010203	0.83[CEU][hapmap];0.86[EUR][1000 genomes];1.00[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	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv832827	chr14:71676178-71833519	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1990035	PCNX	cis	parietal	SCAN
rs1990035	PCNX	cis	cerebellum	SCAN
rs1990035	SLC39A9	cis	parietal	SCAN
rs1990035	SIPA1L1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71680600-71702600	Weak transcription	Brain Angular Gyrus	brain
2	chr14:71687400-71699000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr14:71692000-71698600	Weak transcription	K562	blood
4	chr14:71695000-71696200	Enhancers	HepG2	liver
5	chr14:71695400-71696000	Enhancers	Hela-S3	cervix
6	chr14:71695600-71697400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr14:71695600-71697600	Weak transcription	Esophagus	oesophagus
8	chr14:71695600-71702600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr14:71695800-71709400	Weak transcription	Pancreas	Pancrea

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