Variant report

Variant	rs67040465
Chromosome Location	chr7:100083078-100083079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr7:100082923-100083277	A549	lung:	n/a	n/a
2	NR3C1	chr7:100083015-100083241	A549	lung:	n/a	chr7:100083143-100083157 chr7:100083143-100083158 chr7:100083147-100083160 chr7:100083044-100083057
3	NR3C1	chr7:100082985-100083415	A549	lung:	n/a	chr7:100083249-100083258 chr7:100083143-100083157 chr7:100083143-100083158 chr7:100083147-100083160 chr7:100083044-100083057
4	USF1	chr7:100083029-100083542	H1-hESC	embryonic stem cell:	n/a	chr7:100083314-100083325
5	NR3C1	chr7:100082877-100083389	A549	lung:	n/a	chr7:100083249-100083258 chr7:100083143-100083157 chr7:100083143-100083158 chr7:100083147-100083160 chr7:100083044-100083057
6	CEBPB	chr7:100083025-100083234	HepG2	liver:	n/a	n/a
7	NR3C1	chr7:100082851-100083488	A549	lung:	n/a	chr7:100083249-100083258 chr7:100083143-100083157 chr7:100083143-100083158 chr7:100083147-100083160 chr7:100083044-100083057

No.	Distal block	Cell Line	Cell type
1	chr7:100025812..100027550-chr7:100082592..100085700,3	K562	blood:
2	chr7:100048219..100049829-chr7:100081555..100083506,2	K562	blood:
3	chr7:100081567..100083777-chr7:100163573..100165544,2	K562	blood:
4	chr7:100073820..100078843-chr7:100079329..100083762,6	MCF-7	breast:
5	chr7:100074425..100078694-chr7:100079448..100083758,11	K562	blood:
6	chr7:100024700..100032514-chr7:100067180..100083143,31	K562	blood:
7	chr7:100079431..100084153-chr7:100084209..100089579,10	K562	blood:
8	chr7:100080163..100084843-chr7:100085212..100090254,7	MCF-7	breast:

Variant related genes	Relation type
NYAP1	TF binding region
ENSG00000266372	TF binding region
ENSG00000078487	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000166924	Chromatin interaction
ENSG00000166925	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	0.86[ASN][1000 genomes]
rs11559117	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11760536	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11761624	0.86[ASN][1000 genomes]
rs11761725	0.86[ASN][1000 genomes]
rs11761784	0.86[ASN][1000 genomes]
rs11763511	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11764818	0.86[ASN][1000 genomes]
rs11766202	0.86[ASN][1000 genomes]
rs11766752	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11769700	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11772580	0.86[ASN][1000 genomes]
rs11773661	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1962269	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2406253	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2406255	0.86[ASN][1000 genomes]
rs28629346	0.86[ASN][1000 genomes]
rs2897358	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34989573	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4074838	0.86[ASN][1000 genomes]
rs4385401	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4463351	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4469386	0.86[ASN][1000 genomes]
rs4472444	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4989959	0.86[ASN][1000 genomes]
rs60257855	0.86[ASN][1000 genomes]
rs60478351	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60644673	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60844404	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66648318	0.86[ASN][1000 genomes]
rs66958101	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67196635	0.86[ASN][1000 genomes]
rs67239991	0.86[ASN][1000 genomes]
rs67483801	0.86[ASN][1000 genomes]
rs67885733	0.86[ASN][1000 genomes]
rs6948699	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6953107	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6955362	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6962151	0.86[ASN][1000 genomes]
rs6972167	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6974286	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6975514	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6975729	0.86[ASN][1000 genomes]
rs6978739	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6979335	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73405353	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7787620	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7787825	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7794485	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7800667	0.86[ASN][1000 genomes]
rs7809801	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7811142	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[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
rs67040465	PVRIG2P	cis	Thyroid	GTEx
rs67040465	PVRIG2P	cis	Artery Tibial	GTEx
rs67040465	PILRA	cis	Artery Tibial	GTEx
rs67040465	PILRA	cis	Adipose Subcutaneous	GTEx
rs67040465	PILRB	cis	Artery Tibial	GTEx
rs67040465	STAG3L5P	cis	Thyroid	GTEx
rs67040465	PILRA	cis	Nerve Tibial	GTEx
rs67040465	PILRA	cis	Muscle Skeletal	GTEx
rs67040465	PILRA	cis	Heart Left Ventricle	GTEx
rs67040465	PMS2P1	cis	Thyroid	GTEx
rs67040465	PILRB	cis	Adipose Subcutaneous	GTEx
rs67040465	PILRB	cis	Thyroid	GTEx
rs67040465	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs67040465	PILRA	cis	Thyroid	GTEx
rs67040465	PILRA	cis	Artery Aorta	GTEx
rs67040465	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs67040465	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs67040465	PILRB	cis	Whole Blood	GTEx
rs67040465	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs67040465	PILRA	cis	Esophagus Mucosa	GTEx
rs67040465	STAG3L5P	cis	Muscle Skeletal	GTEx
rs67040465	PILRB	cis	Esophagus Mucosa	GTEx
rs67040465	PILRB	cis	Nerve Tibial	GTEx
rs67040465	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs67040465	STAG3L5P	cis	Nerve Tibial	GTEx
rs67040465	STAG3L5P	cis	Artery Aorta	GTEx
rs67040465	STAG3L5P	cis	Stomach	GTEx
rs67040465	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs67040465	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs67040465	PVRIG2P	cis	lung	GTEx
rs67040465	STAG3L5P	cis	Artery Tibial	GTEx
rs67040465	PILRA	cis	Esophagus Muscularis	GTEx
rs67040465	PILRB	cis	lung	GTEx
rs67040465	PILRB	cis	Muscle Skeletal	GTEx
rs67040465	PILRB	cis	Heart Left Ventricle	GTEx
rs67040465	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs67040465	PVRIG2P	cis	Nerve Tibial	GTEx
rs67040465	PILRB	cis	Artery Aorta	GTEx
rs67040465	PILRB	cis	Esophagus Muscularis	GTEx
rs67040465	STAG3L5P	cis	lung	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100080800-100083200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:100081000-100083200	Active TSS	Brain Cingulate Gyrus	brain
3	chr7:100081000-100083400	Active TSS	Brain Anterior Caudate	brain
4	chr7:100081000-100090600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr7:100081400-100083200	Weak transcription	Spleen	Spleen
6	chr7:100081400-100084200	Enhancers	Hela-S3	cervix
7	chr7:100081800-100083200	Weak transcription	NH-A	brain
8	chr7:100081800-100083200	Weak transcription	Osteobl	bone
9	chr7:100081800-100083800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:100081800-100086800	Weak transcription	Primary T cells from cord blood	blood
11	chr7:100081800-100087400	Weak transcription	NHLF	lung
12	chr7:100081800-100091000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:100081800-100091000	Weak transcription	Right Atrium	heart
14	chr7:100082000-100083600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:100082000-100083600	Enhancers	K562	blood
16	chr7:100082000-100084200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:100082000-100084200	Enhancers	Adipose Nuclei	Adipose
18	chr7:100082000-100086800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:100082000-100086800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr7:100082000-100087400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:100082000-100090800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:100082200-100083200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:100082200-100083400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr7:100082200-100083600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:100082200-100083600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:100082200-100083600	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr7:100082200-100083600	Enhancers	Ovary	ovary
28	chr7:100082200-100084600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:100082200-100085800	Weak transcription	Fetal Intestine Large	intestine
30	chr7:100082200-100086000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:100082200-100087000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:100082200-100090600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr7:100082400-100083200	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr7:100082400-100083600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr7:100082400-100083600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:100082400-100083600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr7:100082400-100083600	Flanking Active TSS	Fetal Brain Female	brain
38	chr7:100082400-100083600	Enhancers	Fetal Lung	lung
39	chr7:100082400-100083800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr7:100082400-100084000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr7:100082400-100084000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:100082400-100084000	Weak transcription	Pancreas	Pancrea
43	chr7:100082400-100084400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:100082400-100084600	Weak transcription	Placenta	Placenta
45	chr7:100082400-100085000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr7:100082400-100085000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr7:100082400-100085000	Genic enhancers	Fetal Stomach	stomach
48	chr7:100082400-100085000	Enhancers	A549	lung
49	chr7:100082400-100085200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr7:100082400-100087400	Weak transcription	H9 Cell Line	embryonic stem cell

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