Variant report

Variant	rs1047720
Chromosome Location	chr9:14588910-14588911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZDHHC21-3	chr9:14588795-14590063	ENSG00000272871.1
2	lnc-C9orf146-7	chr9:14588795-14589277	NONHSAT130249

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10120026	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10125272	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1047717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1047718	0.98[ASN][1000 genomes]
rs10738371	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10756582	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10756591	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10810187	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1130072	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs1343568	0.82[CHB][hapmap]
rs1343571	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1343572	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2382486	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2382487	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2382494	0.84[AFR][1000 genomes]
rs3789018	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3802482	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs4492471	0.86[CHB][hapmap]
rs4620377	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs6474846	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7031926	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs72605692	0.96[ASN][1000 genomes]
rs7849849	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7850885	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7852534	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7857143	0.81[CHB][hapmap]
rs7874535	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv831517	chr9:14512924-14738206	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3362157	chr9:14542189-14791977	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv521363	chr9:14566406-14691897	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv3380008	chr9:14573378-14615933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv892605	chr9:14585052-14709151	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv892606	chr9:14588049-14697022	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1047720	ZDHHC21	cis	cerebellum	SCAN
rs1047720	PSIP1	cis	parietal	SCAN
rs1047720	ZDHHC21	Cis_1M	lymphoblastoid	RTeQTL
rs1047720	CER1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14577400-14597200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:14577600-14596200	Weak transcription	Pancreas	Pancrea
3	chr9:14582400-14596200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:14585200-14589000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:14585800-14598000	Weak transcription	Right Ventricle	heart
6	chr9:14586000-14592000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:14586000-14596200	Weak transcription	Lung	lung
8	chr9:14586000-14597000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr9:14586200-14595200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr9:14586400-14595800	Weak transcription	Brain Germinal Matrix	brain
11	chr9:14586600-14595200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:14586800-14593400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr9:14586800-14629800	Weak transcription	Primary T cells from cord blood	blood
14	chr9:14587200-14591600	Weak transcription	GM12878-XiMat	blood
15	chr9:14587400-14595800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr9:14587600-14595600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:14587600-14596200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:14587600-14596200	Weak transcription	Left Ventricle	heart
19	chr9:14587600-14599600	Weak transcription	Placenta	Placenta
20	chr9:14587800-14618400	Weak transcription	HUVEC	blood vessel
21	chr9:14588000-14596000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:14588200-14589000	Weak transcription	Aorta	Aorta
23	chr9:14588200-14591200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:14588200-14618800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:14588800-14595800	Weak transcription	Liver	Liver
26	chr9:14588800-14595800	Weak transcription	Duodenum Mucosa	Duodenum

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