Variant report

Variant	rs4699033
Chromosome Location	chr4:103818734-103818735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CISD2-6	chr4:103817882-103819394	NONHSAT097617

Extended variants
information (count: 137 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10004342	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10012413	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10015289	0.81[ASN][1000 genomes]
rs10029073	0.81[ASN][1000 genomes]
rs10031181	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10032234	0.81[ASN][1000 genomes]
rs11097796	0.81[ASN][1000 genomes]
rs11097797	0.81[ASN][1000 genomes]
rs11722779	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11731885	0.81[ASN][1000 genomes]
rs11737544	0.81[ASN][1000 genomes]
rs12500379	0.81[ASN][1000 genomes]
rs12501737	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12508069	0.81[ASN][1000 genomes]
rs13113923	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13117110	0.81[ASN][1000 genomes]
rs13136616	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13144033	0.80[ASN][1000 genomes]
rs13150426	0.81[ASN][1000 genomes]
rs1383733	0.81[ASN][1000 genomes]
rs17033381	0.85[ASN][1000 genomes]
rs2086499	0.81[ASN][1000 genomes]
rs28367331	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2866417	0.81[ASN][1000 genomes]
rs28778380	0.81[ASN][1000 genomes]
rs28811632	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28845922	0.81[ASN][1000 genomes]
rs2903284	0.81[ASN][1000 genomes]
rs34506429	0.89[ASN][1000 genomes]
rs34725541	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3843441	0.83[ASN][1000 genomes]
rs3857198	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3857199	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3857200	0.81[ASN][1000 genomes]
rs3886722	0.81[ASN][1000 genomes]
rs3886723	0.81[ASN][1000 genomes]
rs3960788	0.80[ASN][1000 genomes]
rs3974478	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3974481	0.87[ASN][1000 genomes]
rs3974485	0.81[ASN][1000 genomes]
rs3974599	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3974604	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3974605	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3974606	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3974608	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4235407	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4235409	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4334755	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4339216	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4382039	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4446311	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4455413	0.85[ASN][1000 genomes]
rs4455415	0.81[ASN][1000 genomes]
rs4525977	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4530634	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4533776	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4540048	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4623004	0.81[ASN][1000 genomes]
rs4642252	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4645215	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4698864	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4698867	0.89[ASN][1000 genomes]
rs4698874	0.81[ASN][1000 genomes]
rs4699032	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699034	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4699035	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4699037	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4699039	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4699040	0.87[ASN][1000 genomes]
rs4699042	0.80[ASN][1000 genomes]
rs4699044	0.81[ASN][1000 genomes]
rs4699045	0.81[ASN][1000 genomes]
rs4699046	0.81[ASN][1000 genomes]
rs4699047	0.81[ASN][1000 genomes]
rs5028609	0.89[ASN][1000 genomes]
rs6533030	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6533035	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533037	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533046	0.86[ASN][1000 genomes]
rs6533050	0.81[ASN][1000 genomes]
rs6533051	0.81[ASN][1000 genomes]
rs6533052	0.81[ASN][1000 genomes]
rs6810668	0.81[ASN][1000 genomes]
rs6815526	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6815540	0.89[ASN][1000 genomes]
rs6818418	0.85[ASN][1000 genomes]
rs6821173	0.85[ASN][1000 genomes]
rs6821247	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6822658	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6823625	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6824070	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6828072	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6830193	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6830407	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6841492	0.85[ASN][1000 genomes]
rs6846762	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6847093	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6847191	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6852141	0.81[ASN][1000 genomes]
rs6853193	0.81[ASN][1000 genomes]
rs6856176	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs724446	0.81[ASN][1000 genomes]
rs724447	0.81[ASN][1000 genomes]
rs7375679	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7659468	0.83[ASN][1000 genomes]
rs7663876	0.85[ASN][1000 genomes]
rs7665655	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7672319	0.81[ASN][1000 genomes]
rs7676943	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7677003	0.85[ASN][1000 genomes]
rs7678030	0.82[ASN][1000 genomes]
rs7681002	0.82[ASN][1000 genomes]
rs7681629	0.85[ASN][1000 genomes]
rs7682755	0.85[ASN][1000 genomes]
rs7685399	0.81[ASN][1000 genomes]
rs7686957	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7687092	0.81[ASN][1000 genomes]
rs7687707	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7688940	0.81[ASN][1000 genomes]
rs9307280	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9760180	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9917919	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9999303	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594957	chr4:103728010-103870091	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	esv1802717	chr4:103765156-103870091	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv879683	chr4:103785051-103916717	Flanking Active TSS Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	esv1849799	chr4:103787351-103881772	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv528680	chr4:103807720-103832927	Weak transcription Enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv461598	chr4:103807720-103953389	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv594978	chr4:103807720-103953389	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv1821875	chr4:103810823-103895872	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv1798872	chr4:103810823-103898392	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv1804685	chr4:103811491-103881772	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv967779	chr4:103818716-103819396	Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases
14	nsv967780	chr4:103818716-103853306	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4699033	CISD2	cis	Nerve Tibial	GTEx
rs4699033	MANBA	cis	multi-tissue	Pritchard
rs4699033	CISD2	cis	multi-tissue	Pritchard
rs4699033	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs4699033	LRRC37A15P	cis	lung	GTEx
rs4699033	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs4699033	CISD2	cis	Esophagus Muscularis	GTEx
rs4699033	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs4699033	KRT8P46	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103791200-103834800	Weak transcription	Ovary	ovary
2	chr4:103796400-103819800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr4:103799200-103819400	Weak transcription	Thymus	Thymus
4	chr4:103804800-103819000	Weak transcription	K562	blood
5	chr4:103817400-103818800	Weak transcription	HepG2	liver
6	chr4:103818600-103819000	Enhancers	HSMMtube	muscle

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