Variant report

Variant	rs3960788
Chromosome Location	chr4:103915618-103915619
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	chr4:103747264..103750230-chr4:103913899..103916537,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109332	Chromatin interaction
ENSG00000246560	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10004342	0.82[ASN][1000 genomes]
rs10015289	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10029073	0.99[ASN][1000 genomes]
rs10031181	0.81[ASN][1000 genomes]
rs10032234	0.99[ASN][1000 genomes]
rs1080081	0.94[ASN][1000 genomes]
rs11097796	0.99[ASN][1000 genomes]
rs11097797	0.99[ASN][1000 genomes]
rs11722779	0.85[ASN][1000 genomes]
rs11731885	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11737544	0.99[ASN][1000 genomes]
rs11938650	0.94[ASN][1000 genomes]
rs12500379	0.99[ASN][1000 genomes]
rs12501737	0.86[ASN][1000 genomes]
rs12508069	0.99[ASN][1000 genomes]
rs13113923	0.87[ASN][1000 genomes]
rs13117110	0.99[ASN][1000 genomes]
rs13130741	0.87[ASN][1000 genomes]
rs13136616	0.80[ASN][1000 genomes]
rs13144033	0.97[ASN][1000 genomes]
rs13150426	0.98[ASN][1000 genomes]
rs1383733	0.99[ASN][1000 genomes]
rs17033381	0.94[ASN][1000 genomes]
rs17215211	0.94[ASN][1000 genomes]
rs2086499	0.98[ASN][1000 genomes]
rs28367331	0.81[ASN][1000 genomes]
rs28445579	0.97[ASN][1000 genomes]
rs28636930	0.94[ASN][1000 genomes]
rs2866417	0.98[ASN][1000 genomes]
rs28778380	0.98[ASN][1000 genomes]
rs28811632	0.80[ASN][1000 genomes]
rs28845922	0.99[ASN][1000 genomes]
rs2903284	0.99[ASN][1000 genomes]
rs34506429	0.90[ASN][1000 genomes]
rs34725541	0.85[ASN][1000 genomes]
rs3843441	0.92[ASN][1000 genomes]
rs3857198	0.89[ASN][1000 genomes]
rs3857199	0.90[ASN][1000 genomes]
rs3857200	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3886722	0.99[ASN][1000 genomes]
rs3886723	0.98[ASN][1000 genomes]
rs3974478	0.85[ASN][1000 genomes]
rs3974481	0.88[ASN][1000 genomes]
rs3974485	0.99[ASN][1000 genomes]
rs3974604	0.87[ASN][1000 genomes]
rs3974605	0.82[ASN][1000 genomes]
rs3974606	0.84[ASN][1000 genomes]
rs3974608	0.85[ASN][1000 genomes]
rs4235409	0.90[ASN][1000 genomes]
rs4339216	0.87[ASN][1000 genomes]
rs4382039	0.84[ASN][1000 genomes]
rs4446311	0.87[ASN][1000 genomes]
rs4455413	0.94[ASN][1000 genomes]
rs4455415	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4530634	0.87[ASN][1000 genomes]
rs4533776	0.88[ASN][1000 genomes]
rs4540048	0.82[ASN][1000 genomes]
rs4623004	0.99[ASN][1000 genomes]
rs4645215	0.85[ASN][1000 genomes]
rs4698864	0.82[ASN][1000 genomes]
rs4698867	0.90[ASN][1000 genomes]
rs4698874	0.98[ASN][1000 genomes]
rs4699032	0.80[ASN][1000 genomes]
rs4699033	0.80[ASN][1000 genomes]
rs4699035	0.87[ASN][1000 genomes]
rs4699037	0.88[ASN][1000 genomes]
rs4699039	0.90[ASN][1000 genomes]
rs4699040	0.88[ASN][1000 genomes]
rs4699042	0.88[ASN][1000 genomes]
rs4699044	0.98[ASN][1000 genomes]
rs4699045	0.99[ASN][1000 genomes]
rs4699046	0.98[ASN][1000 genomes]
rs4699047	0.98[ASN][1000 genomes]
rs4699049	0.94[ASN][1000 genomes]
rs5028609	0.90[ASN][1000 genomes]
rs6533030	0.81[ASN][1000 genomes]
rs6533035	0.84[ASN][1000 genomes]
rs6533037	0.87[ASN][1000 genomes]
rs6533046	0.92[ASN][1000 genomes]
rs6533050	0.99[ASN][1000 genomes]
rs6533051	0.99[ASN][1000 genomes]
rs6533052	0.99[ASN][1000 genomes]
rs6810668	0.97[ASN][1000 genomes]
rs6815526	0.85[ASN][1000 genomes]
rs6815540	0.90[ASN][1000 genomes]
rs6818418	0.94[ASN][1000 genomes]
rs6821173	0.94[ASN][1000 genomes]
rs6821247	0.87[ASN][1000 genomes]
rs6824070	0.85[ASN][1000 genomes]
rs6828072	0.82[ASN][1000 genomes]
rs6830193	0.90[ASN][1000 genomes]
rs6830407	0.80[ASN][1000 genomes]
rs6841492	0.94[ASN][1000 genomes]
rs6842179	0.94[ASN][1000 genomes]
rs6846762	0.80[ASN][1000 genomes]
rs6847093	0.86[ASN][1000 genomes]
rs6847191	0.84[ASN][1000 genomes]
rs6852141	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6853193	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6856176	0.85[ASN][1000 genomes]
rs724446	0.99[ASN][1000 genomes]
rs724447	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7375679	0.86[ASN][1000 genomes]
rs7659468	0.90[ASN][1000 genomes]
rs7660298	0.92[ASN][1000 genomes]
rs7663876	0.94[ASN][1000 genomes]
rs7665655	0.86[ASN][1000 genomes]
rs7672319	0.99[ASN][1000 genomes]
rs7676736	0.97[ASN][1000 genomes]
rs7676943	0.87[ASN][1000 genomes]
rs7677003	0.94[ASN][1000 genomes]
rs7678030	0.92[ASN][1000 genomes]
rs7681002	0.91[ASN][1000 genomes]
rs7681629	0.94[ASN][1000 genomes]
rs7682755	0.94[ASN][1000 genomes]
rs7685399	0.98[ASN][1000 genomes]
rs7686957	0.85[ASN][1000 genomes]
rs7687092	0.99[ASN][1000 genomes]
rs7687707	0.83[ASN][1000 genomes]
rs7688940	0.98[ASN][1000 genomes]
rs7694724	0.92[ASN][1000 genomes]
rs7695096	0.88[ASN][1000 genomes]
rs7698608	0.97[ASN][1000 genomes]
rs9307280	0.83[ASN][1000 genomes]
rs9760180	0.86[ASN][1000 genomes]
rs9917919	0.86[ASN][1000 genomes]
rs9999303	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv879684	chr4:103887561-103939894	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3960788	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs3960788	CISD2	cis	Nerve Tibial	GTEx
rs3960788	CISD2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103908800-103926600	Weak transcription	Primary T cells from cord blood	blood
2	chr4:103915400-103916200	Weak transcription	Primary B cells from cord blood	blood

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