Variant report

Variant	rs10259748
Chromosome Location	chr7:69281111-69281112
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1008379	0.80[EUR][1000 genomes]
rs1014417	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10245786	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10257549	0.84[ASN][1000 genomes]
rs10452738	0.84[ASN][1000 genomes]
rs11508453	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11761141	0.82[AMR][1000 genomes]
rs11763186	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974201	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11978431	0.84[ASN][1000 genomes]
rs12333974	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12698813	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12698816	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12698822	0.82[AMR][1000 genomes]
rs12698825	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12698830	0.84[ASN][1000 genomes]
rs13226538	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13237811	0.82[ASN][1000 genomes]
rs17140933	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17140980	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17140982	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17353815	0.81[EUR][1000 genomes]
rs1860488	0.92[ASN][1000 genomes]
rs1985165	0.86[ASN][1000 genomes]
rs210591	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs210593	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs210594	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs210596	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs210599	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs210601	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs210604	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs210606	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2533427	0.91[ASN][1000 genomes]
rs2533428	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2533429	0.91[ASN][1000 genomes]
rs2533430	0.86[ASN][1000 genomes]
rs2533431	0.92[ASN][1000 genomes]
rs2533433	0.92[ASN][1000 genomes]
rs2533435	0.87[ASN][1000 genomes]
rs2533449	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2533458	0.92[ASN][1000 genomes]
rs2851483	0.91[ASN][1000 genomes]
rs2851484	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2851487	0.92[ASN][1000 genomes]
rs2851503	0.82[ASN][1000 genomes]
rs2851505	0.81[ASN][1000 genomes]
rs2851506	0.82[ASN][1000 genomes]
rs2851507	0.82[ASN][1000 genomes]
rs2851514	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2851515	0.91[ASN][1000 genomes]
rs2851516	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2865805	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28770244	0.84[ASN][1000 genomes]
rs34221396	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34617709	0.81[AFR][1000 genomes]
rs35696945	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4717520	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4718906	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs505949	0.92[ASN][1000 genomes]
rs513150	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs532820	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs547630	0.92[ASN][1000 genomes]
rs55990156	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565505	0.92[ASN][1000 genomes]
rs576193	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs576293	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs585282	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[ASN][1000 genomes]
rs589983	0.94[ASN][1000 genomes]
rs590609	0.96[ASN][1000 genomes]
rs593063	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs595681	0.87[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs60359704	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60739014	0.81[EUR][1000 genomes]
rs610930	0.87[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs626767	0.92[ASN][1000 genomes]
rs627981	0.92[ASN][1000 genomes]
rs645245	0.92[ASN][1000 genomes]
rs6460532	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs646233	0.91[ASN][1000 genomes]
rs649200	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6943309	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6951921	0.84[ASN][1000 genomes]
rs6955261	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6958981	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6961164	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6963882	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6966036	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6978134	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6979355	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6980307	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs726372	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs763759	0.81[EUR][1000 genomes]
rs7779010	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7786073	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7795152	0.82[ASN][1000 genomes]
rs7796973	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7797340	0.84[ASN][1000 genomes]
rs7801117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7808773	0.81[EUR][1000 genomes]
rs7809145	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809934	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs877687	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9332399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10259748	VKORC1L1	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69265800-69282600	Weak transcription	Pancreas	Pancrea
2	chr7:69276800-69282800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:69277200-69282400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:69277800-69283200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr7:69277800-69285000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr7:69277800-69285000	Enhancers	Fetal Heart	heart
7	chr7:69277800-69286200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:69278400-69286000	Enhancers	Rectal Smooth Muscle	rectum
9	chr7:69279000-69281800	Weak transcription	Fetal Thymus	thymus
10	chr7:69279000-69287000	Weak transcription	GM12878-XiMat	blood
11	chr7:69279200-69282000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:69279800-69281400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:69279800-69281400	Weak transcription	Brain Angular Gyrus	brain
14	chr7:69279800-69281600	Weak transcription	HSMM	muscle
15	chr7:69279800-69282000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:69279800-69282000	Weak transcription	Fetal Brain Male	brain
17	chr7:69279800-69282200	Weak transcription	Right Ventricle	heart
18	chr7:69279800-69282600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:69279800-69282600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:69279800-69282600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:69279800-69282600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:69279800-69282600	Weak transcription	Lung	lung
23	chr7:69279800-69282800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr7:69279800-69283200	Enhancers	NHDF-Ad	bronchial
25	chr7:69279800-69285800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:69279800-69289000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr7:69279800-69289600	Weak transcription	Psoas Muscle	Psoas
28	chr7:69280000-69281200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:69280000-69281200	Enhancers	Brain Germinal Matrix	brain
30	chr7:69280000-69281200	Weak transcription	Placenta	Placenta
31	chr7:69280000-69281800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr7:69280000-69281800	Weak transcription	Fetal Lung	lung
33	chr7:69280000-69282000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr7:69280000-69282000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr7:69280000-69282000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr7:69280000-69282000	Weak transcription	Right Atrium	heart
37	chr7:69280000-69282000	Weak transcription	NH-A	brain
38	chr7:69280000-69282400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:69280000-69282600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr7:69280000-69282600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr7:69280000-69282800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:69280200-69281400	Weak transcription	Brain Hippocampus Middle	brain
43	chr7:69280200-69281400	Weak transcription	Ovary	ovary
44	chr7:69280200-69281400	Weak transcription	HSMMtube	muscle
45	chr7:69280200-69281600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr7:69280200-69281800	Weak transcription	Adipose Nuclei	Adipose
47	chr7:69280200-69281800	Weak transcription	Brain Anterior Caudate	brain
48	chr7:69280200-69281800	Weak transcription	Fetal Brain Female	brain
49	chr7:69280200-69282000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:69280200-69282000	Weak transcription	Brain Substantia Nigra	brain

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