Variant report

Variant	rs10241492
Chromosome Location	chr7:99994813-99994814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 44 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1000215	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085549	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1063945	0.84[ASN][1000 genomes]
rs1073	1.00[CEU][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11559117	1.00[CEU][hapmap]
rs11760536	1.00[CEU][hapmap]
rs11761253	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11761306	0.84[ASN][1000 genomes]
rs11761426	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11761725	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11761784	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11763414	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763511	1.00[CEU][hapmap]
rs11764818	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11765869	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11766752	1.00[CEU][hapmap]
rs11768933	0.84[ASN][1000 genomes]
rs11768967	0.84[ASN][1000 genomes]
rs11769057	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11769700	1.00[CEU][hapmap]
rs11769886	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771241	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771419	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11771799	0.84[ASN][1000 genomes]
rs11771936	0.84[ASN][1000 genomes]
rs11773661	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs1636980	0.84[ASN][1000 genomes]
rs1962269	0.92[CEU][hapmap]
rs1964242	0.84[ASN][1000 genomes]
rs2003507	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108269	0.84[ASN][1000 genomes]
rs2406253	1.00[CEU][hapmap]
rs2406255	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28490152	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495773	0.84[ASN][1000 genomes]
rs28578163	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28629346	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28660238	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680963	0.84[ASN][1000 genomes]
rs3087502	0.84[ASN][1000 genomes]
rs34989573	0.93[CEU][hapmap]
rs35111986	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35986051	0.84[ASN][1000 genomes]
rs3900792	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074838	0.93[CEU][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41280971	0.84[ASN][1000 genomes]
rs4472444	1.00[CEU][hapmap]
rs4989959	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60257855	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61735533	0.84[ASN][1000 genomes]
rs66632384	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67163493	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67196635	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67239991	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67315960	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67471932	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67483801	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs68116612	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945952	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6946768	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6948685	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6953749	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955362	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs6955367	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6957928	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962151	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6965207	0.84[ASN][1000 genomes]
rs6965458	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6970806	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970828	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6975514	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs6975563	0.84[ASN][1000 genomes]
rs6975660	0.84[ASN][1000 genomes]
rs6975729	1.00[CEU][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6979910	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs705866	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs73161759	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73161762	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401443	0.84[ASN][1000 genomes]
rs73401450	0.84[ASN][1000 genomes]
rs73401451	0.84[ASN][1000 genomes]
rs73403312	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7341507	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7783159	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783550	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7786844	0.84[ASN][1000 genomes]
rs7787620	0.92[CEU][hapmap]
rs7792525	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7792959	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7794485	1.00[CEU][hapmap]
rs7795656	0.84[ASN][1000 genomes]
rs7795805	0.84[ASN][1000 genomes]
rs7799894	0.84[ASN][1000 genomes]
rs7799932	0.84[ASN][1000 genomes]
rs7800667	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7803454	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809801	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:44)

SNP	Gene	Cis/trans	Tissue	Source
rs10241492	PILRA	cis	Esophagus Mucosa	GTEx
rs10241492	PILRB	cis	lung	GTEx
rs10241492	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs10241492	STAG3L5P	cis	Stomach	GTEx
rs10241492	PILRB	cis	multi-tissue	Pritchard
rs10241492	PILRA	cis	Muscle Skeletal	GTEx
rs10241492	PILRB	cis	Esophagus Mucosa	GTEx
rs10241492	PILRB	cis	Esophagus Muscularis	GTEx
rs10241492	PILRA	cis	Adipose Subcutaneous	GTEx
rs10241492	STAG3L5P	cis	Artery Aorta	GTEx
rs10241492	STAG3L5P	cis	Nerve Tibial	GTEx
rs10241492	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs10241492	PILRB	cis	Adipose Subcutaneous	GTEx
rs10241492	PILRB	cis	Whole Blood	GTEx
rs10241492	PILRB	cis	Artery Aorta	GTEx
rs10241492	PVRIG2P	cis	Nerve Tibial	GTEx
rs10241492	STAG3L5P	cis	Thyroid	GTEx
rs10241492	PVRIG2P	cis	Artery Tibial	GTEx
rs10241492	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs10241492	PILRB	cis	Artery Tibial	GTEx
rs10241492	PVRIG2P	cis	Thyroid	GTEx
rs10241492	PILRB	cis	Heart Left Ventricle	GTEx
rs10241492	PILRA	cis	Artery Tibial	GTEx
rs10241492	PILRA	cis	Stomach	GTEx
rs10241492	PILRA	cis	Artery Aorta	GTEx
rs10241492	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs10241492	PVRIG2P	cis	Adipose Subcutaneous	GTEx
rs10241492	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs10241492	STAG3L5P	cis	Muscle Skeletal	GTEx
rs10241492	STAG3L5P	cis	lung	GTEx
rs10241492	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs10241492	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs10241492	PILRA	cis	Nerve Tibial	GTEx
rs10241492	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs10241492	PILRB	cis	Muscle Skeletal	GTEx
rs10241492	PILRB	cis	Thyroid	GTEx
rs10241492	PILRA	cis	Heart Left Ventricle	GTEx
rs10241492	STAG3L5P	cis	Artery Tibial	GTEx
rs10241492	PILRA	cis	Thyroid	GTEx
rs10241492	PILRB	cis	Nerve Tibial	GTEx
rs10241492	PVRIG2P	cis	lung	GTEx
rs10241492	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs10241492	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs10241492	PILRA	cis	Esophagus Muscularis	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99940800-100014600	Weak transcription	Right Atrium	heart
2	chr7:99962400-100020600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:99966400-99998000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:99972600-99996000	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:99973000-99999400	Weak transcription	Brain Anterior Caudate	brain
6	chr7:99976200-99998200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:99987800-100025400	Weak transcription	Right Ventricle	heart
8	chr7:99988600-99999800	Weak transcription	Gastric	stomach
9	chr7:99989600-99995400	Weak transcription	Brain Substantia Nigra	brain
10	chr7:99991800-99995000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr7:99993200-99996400	Enhancers	Primary B cells from peripheral blood	blood
12	chr7:99993200-99996600	Enhancers	Primary B cells from cord blood	blood
13	chr7:99993400-99995800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr7:99993600-99995800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr7:99993800-99995800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr7:99993800-99996200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:99993800-99996400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:99994000-99995000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr7:99994000-99995400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr7:99994000-99995600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:99994000-99996000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr7:99994200-99995000	Enhancers	Primary T cells from cord blood	blood
23	chr7:99994200-99995200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr7:99994200-99995400	Enhancers	Dnd41	blood
25	chr7:99994200-99995600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr7:99994200-99996200	Enhancers	Fetal Thymus	thymus
27	chr7:99994400-99995200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:99994400-99995600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr7:99994600-99995000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr7:99994600-99995000	Flanking Active TSS	GM12878-XiMat	blood
31	chr7:99994600-99995400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:99994600-99996200	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr7:99994800-99995000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:99994800-99995000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr7:99994800-99995000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:99994800-99995200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr7:99994800-99995400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr7:99994800-99995400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr7:99994800-99995600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr7:99994800-99995600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr7:99994800-99995600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr7:99994800-99995600	Enhancers	Colonic Mucosa	Colon
43	chr7:99994800-99995600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr7:99994800-99995800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:99994800-99996200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr7:99994800-99996200	Enhancers	Fetal Muscle Leg	muscle
47	chr7:99994800-99996200	Enhancers	Spleen	Spleen
48	chr7:99994800-99996600	Enhancers	Adipose Nuclei	Adipose
49	chr7:99994800-99997000	Enhancers	Ovary	ovary

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