Variant report

Variant	rs7803454
Chromosome Location	chr7:99991548-99991549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99961125..99963572-chr7:99991510..99993149,2	K562	blood:
2	chr7:99990597..99992604-chr7:100020661..100023007,2	MCF-7	breast:
3	chr7:99987127..99989737-chr7:99990266..99992845,2	K562	blood:
4	chr7:99941834..99943595-chr7:99990991..99992805,2	K562	blood:
5	chr7:99991415..99995843-chr7:99995888..100002627,7	K562	blood:
6	chr7:99991415..99995291-chr7:99995877..99999195,3	K562	blood:
7	chr7:99989101..99992789-chr7:99996981..99999855,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZCWPW1-2	chr7:99991320-99991553	NONHSAT122368

No data

Variant related genes	Relation type
ENSG00000078487	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 45 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1000215	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085549	0.84[ASN][1000 genomes]
rs1063945	0.84[ASN][1000 genomes]
rs1073	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11760536	1.00[AFR][1000 genomes]
rs11761253	0.84[ASN][1000 genomes]
rs11761306	0.84[ASN][1000 genomes]
rs11761426	0.84[ASN][1000 genomes]
rs11761725	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11761784	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11763414	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764818	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11765869	0.84[ASN][1000 genomes]
rs11768933	0.84[ASN][1000 genomes]
rs11768967	0.84[ASN][1000 genomes]
rs11769057	0.84[ASN][1000 genomes]
rs11769886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771241	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771419	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11771799	0.84[ASN][1000 genomes]
rs11771936	0.84[ASN][1000 genomes]
rs1636980	0.84[ASN][1000 genomes]
rs1964242	0.84[ASN][1000 genomes]
rs2003507	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108269	0.84[ASN][1000 genomes]
rs2406255	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28490152	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495773	0.84[ASN][1000 genomes]
rs28578163	0.93[EUR][1000 genomes]
rs28629346	0.91[EUR][1000 genomes]
rs28660238	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680963	0.84[ASN][1000 genomes]
rs3087502	0.84[ASN][1000 genomes]
rs35111986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35986051	0.84[ASN][1000 genomes]
rs3900792	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074838	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41280971	0.84[ASN][1000 genomes]
rs4989959	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60257855	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61735533	0.84[ASN][1000 genomes]
rs66632384	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67163493	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67196635	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67239991	0.93[EUR][1000 genomes]
rs67315960	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67471932	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67483801	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs68116612	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946768	0.84[ASN][1000 genomes]
rs6948685	0.84[ASN][1000 genomes]
rs6953749	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955367	0.84[ASN][1000 genomes]
rs6957928	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962151	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6965207	0.84[ASN][1000 genomes]
rs6965458	0.84[ASN][1000 genomes]
rs6970806	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970828	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6975563	0.84[ASN][1000 genomes]
rs6975660	0.84[ASN][1000 genomes]
rs6975729	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6979910	0.84[ASN][1000 genomes]
rs705866	0.84[ASN][1000 genomes]
rs73161759	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73161762	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401443	0.84[ASN][1000 genomes]
rs73401450	0.84[ASN][1000 genomes]
rs73401451	0.84[ASN][1000 genomes]
rs73403312	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7341507	0.84[ASN][1000 genomes]
rs7783159	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783550	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7786844	0.84[ASN][1000 genomes]
rs7792525	0.84[ASN][1000 genomes]
rs7795656	0.84[ASN][1000 genomes]
rs7795805	0.84[ASN][1000 genomes]
rs7799894	0.84[ASN][1000 genomes]
rs7799932	0.84[ASN][1000 genomes]
rs7800667	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
2	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
3	nsv831071	chr7:99918025-100113413	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	287 gene(s)	inside rSNPs	diseases

mRNA abundance (count:45)

SNP	Gene	Cis/trans	Tissue	Source
rs7803454	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs7803454	STAG3	Cis_1M	lymphoblastoid	RTeQTL
rs7803454	PILRB	cis	Nerve Tibial	GTEx
rs7803454	STAG3L5P	cis	Nerve Tibial	GTEx
rs7803454	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs7803454	PILRA	cis	Stomach	GTEx
rs7803454	PILRA	cis	Thyroid	GTEx
rs7803454	PILRB	cis	Whole Blood	GTEx
rs7803454	PILRB	cis	lung	GTEx
rs7803454	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs7803454	PILRA	cis	Artery Tibial	GTEx
rs7803454	PILRB	cis	Esophagus Muscularis	GTEx
rs7803454	STAG3L5P	cis	lung	GTEx
rs7803454	PILRA	cis	Heart Left Ventricle	GTEx
rs7803454	PILRB	cis	multi-tissue	Pritchard
rs7803454	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs7803454	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs7803454	PILRB	cis	Artery Aorta	GTEx
rs7803454	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs7803454	PILRA	cis	Esophagus Mucosa	GTEx
rs7803454	PVRIG2P	cis	lung	GTEx
rs7803454	STAG3L5P	cis	Artery Tibial	GTEx
rs7803454	PILRA	cis	Artery Aorta	GTEx
rs7803454	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs7803454	PILRB	cis	Artery Tibial	GTEx
rs7803454	PVRIG2P	cis	Adipose Subcutaneous	GTEx
rs7803454	STAG3L5P	cis	Muscle Skeletal	GTEx
rs7803454	PILRB	cis	Thyroid	GTEx
rs7803454	PILRA	cis	Muscle Skeletal	GTEx
rs7803454	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs7803454	STAG3L5P	cis	Artery Aorta	GTEx
rs7803454	PVRIG2P	cis	Thyroid	GTEx
rs7803454	PILRA	cis	Adipose Subcutaneous	GTEx
rs7803454	PILRB	cis	Adipose Subcutaneous	GTEx
rs7803454	PVRIG2P	cis	Esophagus Muscularis	GTEx
rs7803454	PILRA	cis	Nerve Tibial	GTEx
rs7803454	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs7803454	PILRB	cis	Heart Left Ventricle	GTEx
rs7803454	PILRA	cis	Esophagus Muscularis	GTEx
rs7803454	STAG3L5P	cis	Thyroid	GTEx
rs7803454	PILRB	cis	Esophagus Mucosa	GTEx
rs7803454	PVRIG2P	cis	Artery Tibial	GTEx
rs7803454	PVRIG2P	cis	Nerve Tibial	GTEx
rs7803454	PILRB	cis	Muscle Skeletal	GTEx
rs7803454	PILRB	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99940800-100014600	Weak transcription	Right Atrium	heart
2	chr7:99962400-100020600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:99966400-99998000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:99972600-99996000	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:99972800-99994800	Weak transcription	Spleen	Spleen
6	chr7:99973000-99999400	Weak transcription	Brain Anterior Caudate	brain
7	chr7:99976200-99998200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:99985400-99994800	Weak transcription	Ovary	ovary
9	chr7:99987800-100025400	Weak transcription	Right Ventricle	heart
10	chr7:99988200-99994200	Weak transcription	Fetal Thymus	thymus
11	chr7:99988600-99994800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:99988600-99994800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:99988600-99994800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:99988600-99999800	Weak transcription	Gastric	stomach
15	chr7:99989600-99993400	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr7:99989600-99995400	Weak transcription	Brain Substantia Nigra	brain
17	chr7:99990600-99992000	Enhancers	Primary B cells from cord blood	blood
18	chr7:99990600-99992000	Enhancers	Primary B cells from peripheral blood	blood
19	chr7:99990800-99991600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr7:99990800-99992000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:99991000-99991800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:99991000-99991800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
23	chr7:99991000-99991800	Flanking Active TSS	GM12878-XiMat	blood
24	chr7:99991400-99991600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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