Variant report

Variant	rs1059129
Chromosome Location	chr7:99926522-99926523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 45 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10085549	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1063945	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11761253	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11761306	0.85[ASN][1000 genomes]
rs11761426	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11765869	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11768933	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11768967	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11769057	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11771419	0.85[ASN][1000 genomes]
rs11771799	0.85[ASN][1000 genomes]
rs11771936	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1636980	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1964242	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108269	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28401739	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28495773	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28680963	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3087502	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35986051	0.85[ASN][1000 genomes]
rs3991498	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3991564	0.85[EUR][1000 genomes]
rs41280971	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61735533	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6945952	0.82[EUR][1000 genomes]
rs6946768	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6948685	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6955367	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6965207	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6965458	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6975563	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6975660	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6979910	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs705866	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73401443	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73401450	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73401451	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7341507	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7783550	0.85[ASN][1000 genomes]
rs7786844	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7792525	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7792959	0.82[EUR][1000 genomes]
rs7795656	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7795805	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799894	0.85[ASN][1000 genomes]
rs7799932	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
2	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
3	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
4	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv888774	chr7:99807265-99951315	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	esv16057	chr7:99809377-99937347	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	esv3379367	chr7:99811760-99938687	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv3379649	chr7:99812207-99939196	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	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
11	esv3358931	chr7:99816130-99943645	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	esv3405423	chr7:99816156-99943860	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	esv3508070	chr7:99816206-99943813	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	esv3508071	chr7:99816206-99943813	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	esv1815812	chr7:99874387-99930879	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv1803899	chr7:99875357-99930879	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
17	esv1817757	chr7:99896488-99935709	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
18	nsv8183	chr7:99896574-99936641	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
19	esv16361	chr7:99898203-99934029	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
20	esv1802263	chr7:99900098-99931667	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
21	esv1832874	chr7:99900098-99931667	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
22	esv1823451	chr7:99900098-99932328	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	esv1797484	chr7:99901968-99932858	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
24	esv1816915	chr7:99901968-99932858	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
25	esv1851409	chr7:99901968-99932858	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
26	esv1830570	chr7:99901968-99945827	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
27	esv1817228	chr7:99904585-99935709	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
28	esv1809006	chr7:99904607-99928168	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
29	nsv970561	chr7:99904859-99936381	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
30	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
31	nsv967347	chr7:99918412-99928137	Weak transcription Strong transcription Genic enhancers Enhancers	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:45)

SNP	Gene	Cis/trans	Tissue	Source
rs1059129	PILRB	cis	Muscle Skeletal	GTEx
rs1059129	PILRA	cis	Muscle Skeletal	GTEx
rs1059129	PILRB	cis	Nerve Tibial	GTEx
rs1059129	PILRA	cis	Nerve Tibial	GTEx
rs1059129	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs1059129	PILRB	cis	Heart Left Ventricle	GTEx
rs1059129	PILRB	cis	Whole Blood	GTEx
rs1059129	PILRB	cis	Thyroid	GTEx
rs1059129	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs1059129	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs1059129	PILRA	cis	Esophagus Muscularis	GTEx
rs1059129	PVRIG2P	cis	Heart Left Ventricle	GTEx
rs1059129	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs1059129	STAG3L5P	cis	Thyroid	GTEx
rs1059129	PVRIG2P	cis	lung	GTEx
rs1059129	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs1059129	PILRA	cis	Artery Aorta	GTEx
rs1059129	PILRB	cis	Artery Tibial	GTEx
rs1059129	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs1059129	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs1059129	STAG3L5P	cis	Artery Aorta	GTEx
rs1059129	PILRA	cis	Thyroid	GTEx
rs1059129	PILRA	cis	Esophagus Mucosa	GTEx
rs1059129	PILRB	cis	Adipose Subcutaneous	GTEx
rs1059129	STAG3	Cis_1M	lymphoblastoid	RTeQTL
rs1059129	STAG3L5P	cis	Stomach	GTEx
rs1059129	PILRA	cis	Stomach	GTEx
rs1059129	PILRA	cis	Adipose Subcutaneous	GTEx
rs1059129	STAG3L5P	cis	Nerve Tibial	GTEx
rs1059129	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs1059129	PILRB	cis	lung	GTEx
rs1059129	PVRIG2P	cis	Nerve Tibial	GTEx
rs1059129	PVRIG2P	cis	Artery Tibial	GTEx
rs1059129	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs1059129	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs1059129	PILRB	cis	Esophagus Muscularis	GTEx
rs1059129	PVRIG2P	cis	Thyroid	GTEx
rs1059129	PILRA	cis	Artery Tibial	GTEx
rs1059129	PVRIG2P	cis	Adipose Subcutaneous	GTEx
rs1059129	PILRB	cis	multi-tissue	Pritchard
rs1059129	STAG3L5P	cis	Artery Tibial	GTEx
rs1059129	STAG3L5P	cis	lung	GTEx
rs1059129	STAG3L5P	cis	Muscle Skeletal	GTEx
rs1059129	PILRB	cis	Esophagus Mucosa	GTEx
rs1059129	PILRA	cis	Heart Left Ventricle	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99870200-99932800	Weak transcription	Ovary	ovary
2	chr7:99870400-99932600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:99870600-99932800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:99874400-99932800	Weak transcription	Brain Angular Gyrus	brain
5	chr7:99887400-99932800	Weak transcription	Brain Anterior Caudate	brain
6	chr7:99896600-99931800	Weak transcription	K562	blood
7	chr7:99897600-99933200	Weak transcription	Pancreas	Pancrea
8	chr7:99898000-99932800	Weak transcription	Brain Substantia Nigra	brain
9	chr7:99902800-99932800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:99911800-99932200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:99912600-99933400	Weak transcription	Fetal Brain Male	brain
12	chr7:99914000-99932800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:99914600-99932800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:99914600-99932800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr7:99914800-99927600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:99915000-99932800	Weak transcription	Brain Hippocampus Middle	brain
17	chr7:99915200-99932800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:99915400-99930800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr7:99915400-99932000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:99915400-99932600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:99915400-99932600	Weak transcription	Primary T cells from cord blood	blood
22	chr7:99915400-99932600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr7:99915600-99932800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:99915600-99932800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr7:99915600-99933200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:99915600-99933200	Weak transcription	Aorta	Aorta
27	chr7:99915800-99930800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr7:99915800-99931600	Weak transcription	Primary B cells from cord blood	blood
29	chr7:99915800-99932000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr7:99915800-99932800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr7:99915800-99932800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr7:99915800-99933000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:99915800-99933200	Weak transcription	Left Ventricle	heart
34	chr7:99916000-99932000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr7:99916000-99932800	Weak transcription	Fetal Kidney	kidney
36	chr7:99916200-99931800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr7:99916200-99932000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr7:99916200-99932800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:99916400-99932800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr7:99916600-99932800	Weak transcription	Right Ventricle	heart
41	chr7:99916600-99932800	Weak transcription	HSMM	muscle
42	chr7:99916800-99932800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr7:99916800-99932800	Weak transcription	Esophagus	oesophagus
44	chr7:99917000-99932800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr7:99917400-99932800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:99918400-99931600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr7:99918600-99931600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr7:99918600-99931800	Weak transcription	Dnd41	blood
49	chr7:99918600-99932800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr7:99918600-99932800	Weak transcription	Fetal Brain Female	brain

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