Variant report

Variant	rs73405353
Chromosome Location	chr7:100091215-100091216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:100090841..100092739-chr7:100123279..100124836,2	K562	blood:
2	chr7:100081775..100084583-chr7:100091175..100094124,2	MCF-7	breast:
3	chr7:100085482..100087607-chr7:100090109..100092006,2	K562	blood:
4	chr7:100083531..100085266-chr7:100090706..100092814,2	K562	blood:
5	chr7:100090031..100091609-chr7:100091866..100094686,2	K562	blood:

Variant related genes	Relation type
ENSG00000166924	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 40 )

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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760536	0.92[AMR][1000 genomes];0.96[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];0.98[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];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769700	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772580	1.00[ASN][1000 genomes]
rs11773661	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962269	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406253	0.92[AMR][1000 genomes];0.96[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34989573	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074838	1.00[ASN][1000 genomes]
rs4385401	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463351	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4469386	1.00[ASN][1000 genomes]
rs4472444	0.88[AMR][1000 genomes];0.93[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60644673	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60844404	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66648318	1.00[ASN][1000 genomes]
rs66958101	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67040465	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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]
rs6948699	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953107	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955362	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962151	1.00[ASN][1000 genomes]
rs6972167	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6974286	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975514	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975729	1.00[ASN][1000 genomes]
rs6978739	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979335	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787620	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787825	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794485	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800667	1.00[ASN][1000 genomes]
rs7809801	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811142	0.82[AMR][1000 genomes];0.92[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:40)

SNP	Gene	Cis/trans	Tissue	Source
rs73405353	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs73405353	PILRB	cis	Thyroid	GTEx
rs73405353	PVRIG2P	cis	lung	GTEx
rs73405353	PILRA	cis	Artery Tibial	GTEx
rs73405353	PMS2P1	cis	Thyroid	GTEx
rs73405353	PILRA	cis	Adipose Subcutaneous	GTEx
rs73405353	PILRB	cis	Adipose Subcutaneous	GTEx
rs73405353	PILRA	cis	Esophagus Muscularis	GTEx
rs73405353	STAG3L5P	cis	Nerve Tibial	GTEx
rs73405353	STAG3L5P	cis	lung	GTEx
rs73405353	PILRB	cis	Artery Aorta	GTEx
rs73405353	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs73405353	STAG3L5P	cis	Artery Tibial	GTEx
rs73405353	PILRB	cis	Artery Tibial	GTEx
rs73405353	PILRA	cis	Thyroid	GTEx
rs73405353	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs73405353	PILRB	cis	lung	GTEx
rs73405353	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs73405353	PVRIG2P	cis	Nerve Tibial	GTEx
rs73405353	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs73405353	PILRB	cis	Heart Left Ventricle	GTEx
rs73405353	PILRB	cis	Whole Blood	GTEx
rs73405353	STAG3L5P	cis	Muscle Skeletal	GTEx
rs73405353	PILRB	cis	Nerve Tibial	GTEx
rs73405353	PILRA	cis	Muscle Skeletal	GTEx
rs73405353	PILRA	cis	Artery Aorta	GTEx
rs73405353	PILRB	cis	Esophagus Muscularis	GTEx
rs73405353	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs73405353	PILRB	cis	Muscle Skeletal	GTEx
rs73405353	PVRIG2P	cis	Thyroid	GTEx
rs73405353	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs73405353	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs73405353	STAG3L5P	cis	Artery Aorta	GTEx
rs73405353	STAG3L5P	cis	Stomach	GTEx
rs73405353	PVRIG2P	cis	Artery Tibial	GTEx
rs73405353	PILRA	cis	Esophagus Mucosa	GTEx
rs73405353	PILRB	cis	Esophagus Mucosa	GTEx
rs73405353	STAG3L5P	cis	Thyroid	GTEx
rs73405353	PILRA	cis	Heart Left Ventricle	GTEx
rs73405353	PILRA	cis	Nerve Tibial	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100082600-100091600	Weak transcription	Fetal Kidney	kidney
2	chr7:100083600-100100800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr7:100085600-100098000	Weak transcription	Hela-S3	cervix
4	chr7:100087000-100091400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:100087200-100091400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:100088800-100104000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:100089200-100095600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:100089800-100091800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:100090000-100092800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:100090400-100092200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:100090800-100091400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:100090800-100091600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr7:100090800-100091800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr7:100090800-100091800	Bivalent/Poised TSS	HepG2	liver
15	chr7:100090800-100092000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
16	chr7:100090800-100092000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:100090800-100092000	Enhancers	Lung	lung
18	chr7:100090800-100092200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
19	chr7:100091000-100091400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr7:100091000-100091400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr7:100091000-100091400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:100091000-100091400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
23	chr7:100091000-100091400	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr7:100091000-100091400	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr7:100091000-100091400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr7:100091000-100091400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr7:100091000-100091400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
28	chr7:100091000-100091400	Flanking Active TSS	Ovary	ovary
29	chr7:100091000-100091400	Flanking Active TSS	Right Ventricle	heart
30	chr7:100091000-100091400	Flanking Active TSS	K562	blood
31	chr7:100091000-100091400	Active TSS	NH-A	brain
32	chr7:100091000-100091600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr7:100091000-100091600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr7:100091000-100091600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:100091000-100091600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr7:100091000-100091600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr7:100091000-100091600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:100091000-100091600	Active TSS	Brain Anterior Caudate	brain
39	chr7:100091000-100091600	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr7:100091000-100091600	Enhancers	Fetal Muscle Trunk	muscle
41	chr7:100091000-100091600	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr7:100091000-100091800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
43	chr7:100091000-100091800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr7:100091000-100091800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:100091000-100091800	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr7:100091000-100091800	Enhancers	Fetal Intestine Large	intestine
47	chr7:100091000-100091800	Enhancers	Placenta	Placenta
48	chr7:100091000-100091800	Enhancers	Pancreas	Pancrea
49	chr7:100091000-100091800	Active TSS	Rectal Smooth Muscle	rectum
50	chr7:100091000-100092000	Active TSS	H9 Cell Line	embryonic stem cell

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