Variant report

Variant	rs6948699
Chromosome Location	chr7:100095349-100095350
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 44 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1073	1.00[ASN][1000 genomes]
rs11559117	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760536	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11761624	1.00[ASN][1000 genomes]
rs11761725	1.00[ASN][1000 genomes]
rs11761784	1.00[ASN][1000 genomes]
rs11763511	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764818	1.00[ASN][1000 genomes]
rs11766202	1.00[ASN][1000 genomes]
rs11766752	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769700	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772580	1.00[ASN][1000 genomes]
rs11773661	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962269	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406253	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406255	1.00[ASN][1000 genomes]
rs28629346	1.00[ASN][1000 genomes]
rs2897358	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34989573	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074838	1.00[ASN][1000 genomes]
rs4385401	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463351	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4469386	1.00[ASN][1000 genomes]
rs4472444	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4989959	1.00[ASN][1000 genomes]
rs60257855	1.00[ASN][1000 genomes]
rs60478351	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60644673	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60844404	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66648318	1.00[ASN][1000 genomes]
rs66958101	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67040465	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67196635	1.00[ASN][1000 genomes]
rs67239991	1.00[ASN][1000 genomes]
rs67483801	1.00[ASN][1000 genomes]
rs67885733	1.00[ASN][1000 genomes]
rs6953107	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955362	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962151	1.00[ASN][1000 genomes]
rs6972167	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6974286	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975514	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975729	1.00[ASN][1000 genomes]
rs6978739	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979335	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405353	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787620	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787825	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794485	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800667	1.00[ASN][1000 genomes]
rs7809801	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811142	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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	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
4	nsv888776	chr7:100014711-100198386	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
5	nsv888777	chr7:100014711-100221867	Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
6	nsv888778	chr7:100014711-100236593	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
7	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
8	nsv888780	chr7:100032665-100198386	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
9	nsv527050	chr7:100056166-100125975	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv888781	chr7:100060928-100097895	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv888782	chr7:100064719-100236593	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
12	nsv888783	chr7:100073292-100136241	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv888784	chr7:100076614-100097895	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:44)

SNP	Gene	Cis/trans	Tissue	Source
rs6948699	PILRA	cis	Thyroid	GTEx
rs6948699	STAG3L5P	cis	Thyroid	GTEx
rs6948699	PILRB	cis	Thyroid	GTEx
rs6948699	PILRB	cis	Esophagus Mucosa	GTEx
rs6948699	PILRB	cis	Nerve Tibial	GTEx
rs6948699	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs6948699	STAG3L5P	cis	Artery Tibial	GTEx
rs6948699	STAG3L5P	cis	Nerve Tibial	GTEx
rs6948699	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs6948699	PILRA	cis	Heart Left Ventricle	GTEx
rs6948699	PILRA	cis	Artery Tibial	GTEx
rs6948699	PILRB	cis	Heart Left Ventricle	GTEx
rs6948699	STAG3L5P	cis	Stomach	GTEx
rs6948699	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs6948699	PILRB	cis	Whole Blood	GTEx
rs6948699	PILRA	cis	Artery Aorta	GTEx
rs6948699	PILRA	cis	Esophagus Mucosa	GTEx
rs6948699	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs6948699	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs6948699	PILRB	cis	Artery Tibial	GTEx
rs6948699	PILRB	cis	Esophagus Muscularis	GTEx
rs6948699	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs6948699	PMS2P1	cis	Thyroid	GTEx
rs6948699	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs6948699	STAG3L5P	cis	Muscle Skeletal	GTEx
rs6948699	PVRIG2P	cis	lung	GTEx
rs6948699	PILRA	cis	Muscle Skeletal	GTEx
rs6948699	PILRB	cis	lung	GTEx
rs6948699	PILRA	cis	Nerve Tibial	GTEx
rs6948699	PILRB	cis	Adipose Subcutaneous	GTEx
rs6948699	PILRB	cis	Muscle Skeletal	GTEx
rs6948699	PILRA	cis	Adipose Subcutaneous	GTEx
rs6948699	PVRIG2P	cis	Adipose Subcutaneous	GTEx
rs6948699	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs6948699	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs6948699	PILRB	cis	Artery Aorta	GTEx
rs6948699	PILRA	cis	Esophagus Muscularis	GTEx
rs6948699	STAG3L5P	cis	lung	GTEx
rs6948699	STAG3L5P	cis	Artery Aorta	GTEx
rs6948699	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs6948699	PVRIG2P	cis	Thyroid	GTEx
rs6948699	PVRIG2P	cis	Nerve Tibial	GTEx
rs6948699	PVRIG2P	cis	Artery Tibial	GTEx
rs6948699	PILRA	cis	Stomach	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100083600-100100800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr7:100085600-100098000	Weak transcription	Hela-S3	cervix
3	chr7:100088800-100104000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:100089200-100095600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:100091800-100100400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:100091800-100100600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:100091800-100136200	Weak transcription	Right Atrium	heart
8	chr7:100092000-100095600	Weak transcription	Fetal Brain Female	brain
9	chr7:100092000-100101000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:100092200-100099400	Weak transcription	NHDF-Ad	bronchial
11	chr7:100092200-100104200	Weak transcription	Fetal Brain Male	brain
12	chr7:100092600-100099400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:100092600-100104000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr7:100092600-100107000	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:100092800-100096400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:100092800-100100600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:100092800-100103800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:100093400-100097000	Weak transcription	Fetal Stomach	stomach
19	chr7:100093400-100100400	Weak transcription	HepG2	liver
20	chr7:100094000-100107000	Weak transcription	Brain Germinal Matrix	brain

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