Variant report

Variant	rs9540996
Chromosome Location	chr13:67670368-67670369
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1022866	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10492596	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10492597	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10507741	0.82[CEU][hapmap]
rs11148737	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11148738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12184632	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12184736	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12372837	0.85[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323911	1.00[JPT][hapmap]
rs1323917	1.00[JPT][hapmap]
rs1323923	1.00[JPT][hapmap]
rs1408170	1.00[JPT][hapmap]
rs1408171	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs149448	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs155010	1.00[CHD][hapmap]
rs17195259	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17195266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17517286	0.82[CEU][hapmap]
rs17517438	0.82[CEU][hapmap];1.00[CHD][hapmap]
rs17587572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17589427	0.82[CEU][hapmap];1.00[CHD][hapmap]
rs17791001	1.00[JPT][hapmap]
rs17791056	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs1924309	1.00[JPT][hapmap]
rs1924310	1.00[JPT][hapmap]
rs1927812	1.00[CHD][hapmap]
rs260131	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs260139	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs260140	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs260160	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs260162	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs260164	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs260165	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs260168	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2875517	1.00[CHD][hapmap]
rs56226179	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56309321	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56915128	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61191692	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959247	0.96[EUR][1000 genomes]
rs61959248	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61959249	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61959360	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61959362	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61959363	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959367	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959407	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61961771	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61961774	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7330064	1.00[CHD][hapmap]
rs7981987	1.00[JPT][hapmap]
rs7987190	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7987478	1.00[JPT][hapmap]
rs7999949	1.00[CHD][hapmap]
rs9317632	1.00[JPT][hapmap]
rs9317633	1.00[JPT][hapmap]
rs9317637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9529158	1.00[JPT][hapmap]
rs9529163	0.85[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9529166	0.93[EUR][1000 genomes]
rs9529167	0.93[EUR][1000 genomes]
rs9529169	0.93[EUR][1000 genomes]
rs9529170	1.00[JPT][hapmap]
rs9529174	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9529180	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9529181	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9529182	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9529183	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9529185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9529186	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9529187	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9529188	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9529190	1.00[CHD][hapmap]
rs9540949	1.00[JPT][hapmap]
rs9540952	1.00[JPT][hapmap]
rs9540953	1.00[JPT][hapmap]
rs9540954	1.00[JPT][hapmap]
rs9540960	1.00[JPT][hapmap]
rs9540964	0.83[EUR][1000 genomes]
rs9540967	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9540968	0.92[EUR][1000 genomes]
rs9540969	0.93[EUR][1000 genomes]
rs9540971	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs9540980	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9540982	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540983	1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540984	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540987	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540989	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540993	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540994	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540997	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9540998	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9540999	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9541000	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9541001	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9541002	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9541003	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9541004	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs9541006	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9541007	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9541008	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9541012	1.00[CHD][hapmap]
rs9541013	0.82[CEU][hapmap];1.00[CHD][hapmap]
rs9541015	0.82[CEU][hapmap]
rs9571705	1.00[JPT][hapmap]
rs9645951	0.83[EUR][1000 genomes]
rs972419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530605	chr13:67126136-67697306	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1035741	chr13:67212973-68077950	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv541817	chr13:67212973-68077950	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv900414	chr13:67515590-67701341	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1045093	chr13:67517932-67693875	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv541821	chr13:67517932-67693875	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv430581	chr13:67572850-67762288	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv430582	chr13:67589898-67762299	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1037217	chr13:67589937-67728156	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1039600	chr13:67593961-67726047	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv541823	chr13:67593961-67726047	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv1040715	chr13:67668189-67699198	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9540996	PCDH9	cis	Nerve Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67665800-67673000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr13:67666200-67675000	Weak transcription	HSMMtube	muscle
3	chr13:67667800-67678600	Enhancers	Brain Substantia Nigra	brain
4	chr13:67668200-67670800	Enhancers	Brain Hippocampus Middle	brain
5	chr13:67668600-67670800	Enhancers	Brain Anterior Caudate	brain
6	chr13:67668600-67671000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr13:67669000-67670400	Active TSS	A549	lung
8	chr13:67669200-67676000	Weak transcription	Adipose Nuclei	Adipose
9	chr13:67669400-67674600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:67669800-67673800	Enhancers	Hela-S3	cervix
11	chr13:67670000-67671800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:67670200-67671000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:67670200-67671000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr13:67670200-67672000	Weak transcription	Brain Angular Gyrus	brain

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