Variant report

Variant	rs11622578
Chromosome Location	chr14:71623715-71623716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10162332	1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs10162513	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1017023	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1017024	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11158894	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11158895	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11628267	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12433285	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12433881	0.81[AMR][1000 genomes]
rs12433971	0.86[AMR][1000 genomes]
rs12436140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12436994	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12437099	0.86[AMR][1000 genomes]
rs12586505	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12591005	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17177802	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17767137	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2003488	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2079305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55831429	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55968807	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55979041	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56369736	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72726621	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72726627	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72726634	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs740069	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs740070	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs740071	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs740072	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs917063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv565043	chr14:71395604-71625112	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1036929	chr14:71469148-71683412	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11622578	TTC9	cis	parietal	SCAN
rs11622578	PCNX	cis	cerebellum	SCAN
rs11622578	PCNX	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71622600-71630400	Weak transcription	Fetal Kidney	kidney
2	chr14:71622800-71623800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:71623600-71624000	Enhancers	Brain Germinal Matrix	brain

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