Variant report

Variant	rs66958101
Chromosome Location	chr7:100074020-100074021
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100072849..100075078-chr7:100283693..100285830,2	K562	blood:
2	chr7:100072419..100074734-chr7:100181421..100183838,2	K562	blood:
3	chr7:100025583..100035841-chr7:100071553..100080023,19	MCF-7	breast:
4	chr7:100072183..100074781-chr7:100075477..100078153,2	K562	blood:
5	chr7:100073820..100078843-chr7:100079329..100083762,6	MCF-7	breast:
6	chr7:100072681..100074818-chr7:100183478..100186083,2	MCF-7	breast:
7	chr7:100070743..100075629-chr7:100178965..100183270,7	K562	blood:
8	chr7:100072828..100074767-chr7:100164156..100166742,3	K562	blood:
9	chr7:100024700..100032514-chr7:100067180..100083143,31	K562	blood:
10	chr7:100022010..100030260-chr7:100068697..100082544,31	K562	blood:
11	chr7:100073864..100076959-chr7:100134677..100138430,3	K562	blood:
12	chr7:100071827..100074750-chr7:100153997..100156937,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000160813	Chromatin interaction
ENSG00000166925	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000146830	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000266372	Chromatin interaction
ENSG00000106351	Chromatin interaction
ENSG00000241357	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000166924	Chromatin interaction
ENSG00000240211	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 41 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1000215	0.81[EUR][1000 genomes]
rs1073	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11559117	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760536	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11761624	1.00[ASN][1000 genomes]
rs11761725	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761784	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763414	0.81[EUR][1000 genomes]
rs11763511	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764818	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766202	1.00[ASN][1000 genomes]
rs11766752	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769700	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772580	1.00[ASN][1000 genomes]
rs11773661	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962269	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003507	0.81[EUR][1000 genomes]
rs2406253	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406255	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28490152	0.81[EUR][1000 genomes]
rs28629346	1.00[ASN][1000 genomes]
rs28660238	0.81[EUR][1000 genomes]
rs2897358	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34989573	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3900792	0.81[EUR][1000 genomes]
rs4074838	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4385401	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463351	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4469386	1.00[ASN][1000 genomes]
rs4472444	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4989959	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60257855	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60478351	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60644673	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60844404	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66632384	0.81[EUR][1000 genomes]
rs66648318	1.00[ASN][1000 genomes]
rs67040465	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67163493	0.81[EUR][1000 genomes]
rs67196635	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67239991	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67315960	0.81[EUR][1000 genomes]
rs67471932	0.81[EUR][1000 genomes]
rs67483801	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67885733	1.00[ASN][1000 genomes]
rs68116612	0.81[EUR][1000 genomes]
rs6948699	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953107	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955362	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957928	0.81[EUR][1000 genomes]
rs6962151	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970806	0.81[EUR][1000 genomes]
rs6972167	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6974286	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975514	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975729	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978739	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979335	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73161759	0.81[EUR][1000 genomes]
rs73403312	0.81[EUR][1000 genomes]
rs73405353	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783159	0.81[EUR][1000 genomes]
rs7787620	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787825	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794485	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800667	1.00[ASN][1000 genomes]
rs7809801	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811142	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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	nsv984550	chr7:100034415-100080060	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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

mRNA abundance (count:41)

SNP	Gene	Cis/trans	Tissue	Source
rs66958101	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs66958101	PILRB	cis	Muscle Skeletal	GTEx
rs66958101	PILRA	cis	Adipose Subcutaneous	GTEx
rs66958101	STAG3L5P	cis	lung	GTEx
rs66958101	PVRIG2P	cis	Artery Tibial	GTEx
rs66958101	PILRA	cis	Heart Left Ventricle	GTEx
rs66958101	STAG3L5P	cis	Thyroid	GTEx
rs66958101	PILRA	cis	Esophagus Mucosa	GTEx
rs66958101	PVRIG2P	cis	Nerve Tibial	GTEx
rs66958101	PILRA	cis	Nerve Tibial	GTEx
rs66958101	PVRIG2P	cis	lung	GTEx
rs66958101	PILRA	cis	Muscle Skeletal	GTEx
rs66958101	PILRB	cis	Esophagus Mucosa	GTEx
rs66958101	PILRA	cis	Artery Aorta	GTEx
rs66958101	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs66958101	PVRIG2P	cis	Thyroid	GTEx
rs66958101	STAG3L5P	cis	Nerve Tibial	GTEx
rs66958101	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs66958101	PMS2P1	cis	Thyroid	GTEx
rs66958101	PILRB	cis	Artery Aorta	GTEx
rs66958101	PILRB	cis	Nerve Tibial	GTEx
rs66958101	PILRB	cis	Esophagus Muscularis	GTEx
rs66958101	STAG3L5P	cis	Muscle Skeletal	GTEx
rs66958101	PILRA	cis	Thyroid	GTEx
rs66958101	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs66958101	PILRB	cis	Whole Blood	GTEx
rs66958101	PILRB	cis	Heart Left Ventricle	GTEx
rs66958101	PILRA	cis	Esophagus Muscularis	GTEx
rs66958101	PILRB	cis	Adipose Subcutaneous	GTEx
rs66958101	PILRA	cis	Artery Tibial	GTEx
rs66958101	STAG3L5P	cis	Artery Tibial	GTEx
rs66958101	PVRIG2P	cis	Adipose Subcutaneous	GTEx
rs66958101	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs66958101	STAG3L5P	cis	Artery Aorta	GTEx
rs66958101	PILRB	cis	lung	GTEx
rs66958101	PILRA	cis	Stomach	GTEx
rs66958101	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs66958101	PILRB	cis	Artery Tibial	GTEx
rs66958101	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs66958101	PILRB	cis	Thyroid	GTEx
rs66958101	STAG3L5P	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100065000-100074800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:100065800-100075200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:100067400-100074400	Weak transcription	Psoas Muscle	Psoas
4	chr7:100067400-100074800	Weak transcription	Aorta	Aorta
5	chr7:100070000-100075400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:100070200-100074600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:100070400-100074600	Genic enhancers	Spleen	Spleen
8	chr7:100071000-100074200	Weak transcription	Small Intestine	intestine
9	chr7:100071000-100074800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr7:100071200-100074200	Weak transcription	Fetal Brain Female	brain
11	chr7:100071800-100075800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:100072400-100074200	Weak transcription	Gastric	stomach
13	chr7:100072600-100074800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:100072600-100075400	Weak transcription	Fetal Kidney	kidney
15	chr7:100072800-100074200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr7:100072800-100074200	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr7:100073000-100074200	Genic enhancers	Dnd41	blood
18	chr7:100073000-100074400	Genic enhancers	Fetal Lung	lung
19	chr7:100073000-100075000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:100073000-100075400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:100073200-100074200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
22	chr7:100073200-100074200	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:100073200-100074200	Genic enhancers	Brain Germinal Matrix	brain
24	chr7:100073200-100074200	Genic enhancers	Pancreas	Pancrea
25	chr7:100073200-100074400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr7:100073200-100074400	Enhancers	Brain Substantia Nigra	brain
27	chr7:100073200-100074400	Enhancers	HMEC	breast
28	chr7:100073200-100074800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:100073200-100074800	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
30	chr7:100073200-100074800	Transcr. at gene 5' and 3'	K562	blood
31	chr7:100073200-100075000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr7:100073200-100075000	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:100073200-100075000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:100073200-100075000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
35	chr7:100073200-100075200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
36	chr7:100073200-100075200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr7:100073200-100075200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:100073200-100075200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
39	chr7:100073200-100075600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:100073200-100076800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
41	chr7:100073400-100074200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr7:100073400-100074200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr7:100073400-100074400	Enhancers	Ovary	ovary
44	chr7:100073400-100074400	Enhancers	NH-A	brain
45	chr7:100073400-100074600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
46	chr7:100073400-100074600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
47	chr7:100073400-100074600	Transcr. at gene 5' and 3'	Hela-S3	cervix
48	chr7:100073400-100074800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr7:100073400-100074800	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr7:100073400-100074800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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