Variant report

Variant	rs17767296
Chromosome Location	chr14:71686784-71686785
allele	A/T
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	JUND	chr14:71686743-71686810	HepG2	liver:	n/a	chr14:71686746-71686757

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIPA1L1-4	chr14:71685817-71689441	ENSG00000269945.1

Variant related genes	Relation type
ENSG00000267901	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10130213	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158898	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11844320	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11850267	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11851589	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109116	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177822	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767266	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990035	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]
rs4899390	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902916	0.89[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	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902922	0.98[AFR][1000 genomes];1.00[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	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60536344	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61174376	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989207	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989208	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574006	0.89[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	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146169	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156194	0.93[MEX][hapmap]
rs72726657	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72726677	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005089	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs8005615	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005925	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010203	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8017895	0.82[AMR][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
rs17767296	PCNX	cis	parietal	SCAN
rs17767296	SIPA1L1	cis	cerebellum	SCAN
rs17767296	SLC39A9	cis	parietal	SCAN
rs17767296	PCNX	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71680600-71702600	Weak transcription	Brain Angular Gyrus	brain
2	chr14:71680800-71691600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr14:71680800-71691800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr14:71682400-71687200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:71682600-71694800	Weak transcription	Pancreas	Pancrea
6	chr14:71685000-71687000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr14:71685400-71686800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr14:71686000-71687400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr14:71686000-71689000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr14:71686200-71688400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr14:71686600-71687400	Enhancers	Spleen	Spleen

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