Variant report

Variant	rs61959248
Chromosome Location	chr13:67623057-67623058
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	chr13:67620328..67623105-chr13:67624007..67626325,2	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10492596	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10492597	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11148737	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11148738	0.96[EUR][1000 genomes]
rs12184632	0.90[EUR][1000 genomes]
rs12184736	0.90[EUR][1000 genomes]
rs12372837	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1408171	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs149448	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17195259	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17195266	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17587572	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17791056	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs260131	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs260139	0.82[ASN][1000 genomes]
rs260140	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs260160	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260162	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260164	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260165	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260168	0.82[ASN][1000 genomes]
rs56226179	0.90[EUR][1000 genomes]
rs56309321	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56915128	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61191692	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61959247	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61959249	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959360	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61959362	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61959363	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61959367	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61959407	0.88[EUR][1000 genomes]
rs61961771	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961774	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9317633	0.81[ASN][1000 genomes]
rs9317637	0.96[EUR][1000 genomes]
rs9529163	0.87[EUR][1000 genomes]
rs9529166	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9529167	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9529169	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9529174	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9529180	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9529181	0.82[ASN][1000 genomes]
rs9529182	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9529183	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9529185	0.96[EUR][1000 genomes]
rs9529186	0.87[EUR][1000 genomes]
rs9529187	0.90[EUR][1000 genomes]
rs9529188	0.86[EUR][1000 genomes]
rs9540964	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9540967	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9540968	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9540969	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9540971	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9540980	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540982	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9540983	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9540984	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9540987	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9540988	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9540989	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9540993	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9540994	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9540995	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9540996	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9540997	0.90[EUR][1000 genomes]
rs9540998	0.90[EUR][1000 genomes]
rs9540999	0.90[EUR][1000 genomes]
rs9541000	0.90[EUR][1000 genomes]
rs9541001	0.81[EUR][1000 genomes]
rs9541002	0.90[EUR][1000 genomes]
rs9541003	0.90[EUR][1000 genomes]
rs9541004	0.90[EUR][1000 genomes]
rs9541006	0.88[EUR][1000 genomes]
rs9541007	0.88[EUR][1000 genomes]
rs9541008	0.88[EUR][1000 genomes]
rs9645951	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs972419	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv832640	chr13:67460304-67635966	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv428604	chr13:67480426-67645030	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61959248	PCDH9	cis	Nerve Tibial	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67616600-67625400	Enhancers	Brain Cingulate Gyrus	brain
2	chr13:67618400-67623800	Enhancers	Brain Anterior Caudate	brain
3	chr13:67619800-67625000	Enhancers	Fetal Lung	lung
4	chr13:67621000-67626600	Enhancers	Brain Hippocampus Middle	brain
5	chr13:67621200-67623400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr13:67621200-67625400	Enhancers	Brain Substantia Nigra	brain
7	chr13:67621800-67623200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr13:67621800-67623800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:67622000-67623600	Enhancers	A549	lung
10	chr13:67622000-67623800	Enhancers	NH-A	brain
11	chr13:67622200-67623200	Enhancers	Primary T cells from cord blood	blood
12	chr13:67622200-67623200	Enhancers	Fetal Stomach	stomach
13	chr13:67622200-67623200	Enhancers	Thymus	Thymus
14	chr13:67622200-67623800	Enhancers	Fetal Thymus	thymus
15	chr13:67622200-67623800	Enhancers	Stomach Mucosa	stomach
16	chr13:67622200-67624800	Enhancers	Fetal Kidney	kidney
17	chr13:67622200-67625400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr13:67622400-67623200	Enhancers	HSMMtube	muscle
19	chr13:67622400-67623400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr13:67622400-67631400	Weak transcription	Psoas Muscle	Psoas
21	chr13:67622600-67623200	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr13:67622600-67623200	Flanking Active TSS	Osteobl	bone
23	chr13:67622600-67623600	Enhancers	Dnd41	blood
24	chr13:67622600-67623800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr13:67622800-67623400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr13:67623000-67623800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr13:67623000-67625000	Weak transcription	Fetal Brain Male	brain
28	chr13:67623000-67625400	Enhancers	Brain Angular Gyrus	brain
29	chr13:67623000-67626600	Weak transcription	Fetal Brain Female	brain

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