Variant report

Variant	rs13226426
Chromosome Location	chr7:64285288-64285289
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10085758	0.83[ASN][1000 genomes]
rs10155953	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10231007	0.90[ASN][1000 genomes]
rs10244479	0.94[ASN][1000 genomes]
rs10251806	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10267321	0.82[AMR][1000 genomes]
rs10267350	0.82[AMR][1000 genomes]
rs10949946	0.86[EUR][1000 genomes]
rs10949947	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10949948	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11974982	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154509	0.84[AMR][1000 genomes]
rs13228575	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13230564	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1464927	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1464928	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1815166	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1815167	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1880656	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2015939	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2418465	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2863927	0.83[ASN][1000 genomes]
rs28878851	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3763506	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4273745	0.81[AMR][1000 genomes]
rs4386865	0.83[AMR][1000 genomes]
rs4518551	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4613868	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4717217	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718125	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4718131	0.82[EUR][1000 genomes]
rs4718142	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56004721	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56075681	0.82[EUR][1000 genomes]
rs57570718	0.82[EUR][1000 genomes]
rs60113999	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6460195	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7781361	0.85[ASN][1000 genomes]
rs7783765	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7785735	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7787287	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7789149	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7790203	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7792444	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7793057	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7802289	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7809177	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7810067	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
4	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv888271	chr7:63961212-64295884	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
7	nsv888273	chr7:63990100-64291622	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
8	nsv888274	chr7:63990100-64331123	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
9	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv888279	chr7:64094285-64331123	Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
12	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv1026390	chr7:64240323-64414364	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
14	nsv888281	chr7:64250409-64295884	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv1033291	chr7:64273434-64406276	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs13226426	SEPHS1P1	cis	Artery Tibial	GTEx
rs13226426	RP11-460N20.5	cis	Adipose Subcutaneous	GTEx
rs13226426	SEPHS1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs13226426	SEPHS1P1	cis	Thyroid	GTEx
rs13226426	RP11-797H7.5	cis	Nerve Tibial	GTEx
rs13226426	SEPHS1P1	cis	Esophagus Muscularis	GTEx
rs13226426	RP11-797H7.3	cis	Whole Blood	GTEx
rs13226426	RP11-797H7.3	cis	Muscle Skeletal	GTEx
rs13226426	RP11-797H7.3	cis	Artery Aorta	GTEx
rs13226426	RP11-797H7.3	cis	Adipose Subcutaneous	GTEx
rs13226426	RP11-797H7.3	cis	Nerve Tibial	GTEx
rs13226426	RP11-797H7.3	cis	lung	GTEx
rs13226426	SEPHS1P1	cis	Nerve Tibial	GTEx
rs13226426	SEPHS1P1	cis	Adipose Subcutaneous	GTEx
rs13226426	RP11-797H7.3	cis	Thyroid	GTEx
rs13226426	RP11-460N20.5	cis	Thyroid	GTEx
rs13226426	RP11-797H7.3	cis	Artery Tibial	GTEx
rs13226426	RP11-797H7.5	cis	lung	GTEx
rs13226426	SEPHS1P1	cis	Muscle Skeletal	GTEx
rs13226426	RP11-797H7.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13226426	INTS4L1	cis	Skin Sun Exposed Lower leg	GTEx
rs13226426	RP11-797H7.3	cis	Esophagus Mucosa	GTEx
rs13226426	RP11-460N20.5	cis	Artery Aorta	GTEx
rs13226426	RP11-797H7.3	cis	Heart Left Ventricle	GTEx
rs13226426	RP11-797H7.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64255800-64293200	Weak transcription	NH-A	brain
2	chr7:64255800-64293400	Weak transcription	Psoas Muscle	Psoas
3	chr7:64256000-64294400	Weak transcription	Fetal Kidney	kidney
4	chr7:64256800-64286200	Weak transcription	Brain Substantia Nigra	brain
5	chr7:64256800-64292200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:64260600-64286200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:64260600-64288800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr7:64260600-64292400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:64260800-64286400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:64260800-64288600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr7:64260800-64291400	Weak transcription	Liver	Liver
12	chr7:64261000-64295400	Weak transcription	Osteobl	bone
13	chr7:64262800-64291400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:64265400-64286400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr7:64268600-64286200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr7:64268600-64296000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:64268800-64292200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr7:64268800-64293400	Weak transcription	Brain Angular Gyrus	brain
19	chr7:64269000-64286200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:64272400-64291200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:64272400-64292800	Weak transcription	Brain Anterior Caudate	brain
22	chr7:64272600-64286200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:64272600-64291200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr7:64272800-64291800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:64272800-64295200	Weak transcription	Fetal Thymus	thymus
26	chr7:64273000-64291200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:64273000-64292800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:64273200-64290600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr7:64273400-64301400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:64273600-64291400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr7:64273600-64292200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr7:64273800-64291800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:64275600-64294000	Weak transcription	Fetal Brain Male	brain
34	chr7:64275800-64286200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr7:64276200-64291200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr7:64276600-64291400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr7:64277800-64292200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:64278000-64288000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr7:64278000-64288200	Weak transcription	K562	blood
40	chr7:64278000-64288800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr7:64278000-64289400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:64278000-64290400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr7:64278000-64291800	Weak transcription	HSMM	muscle
44	chr7:64278000-64293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:64280600-64290200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:64282800-64285600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:64283400-64285400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr7:64283400-64287000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:64283800-64287200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr7:64284000-64285400	Strong transcription	Left Ventricle	heart

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